PDB Short entry for 5FYT HEADER OXIDOREDUCTASE 09-MAR-16 5FYT TITLE CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN COMPLEX TITLE 2 WITH 3D FRAGMENT (5-FLUORO-2-OXO-2,3-DIHYDRO-1H-INDOL-3-YL)ACETIC TITLE 3 ACID (N09996A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJC DOMAIN, UNP RESIDUES 26-101,374-770; COMPND 5 SYNONYM: CANCER/TESTIS ANTIGEN 31, CT31, HISTONE DEMETHYLASE JARID1B, COMPND 6 JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1B, PLU-1, RETINOBLASTOMA- COMPND 7 BINDING PROTEIN 2 HOMOLOG 1, RBP2-H1, LYSINE-SPECIFIC DEMETHYLASE 5B; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PFB-LIC-BSE KEYWDS OXIDOREDUCTASE, JARID1B, PLU1, PANDDA, FRAGMENT SOAKING, X-RAY KEYWDS 2 FRAGMENT SCREENING, STRUCTURAL GENOMICS CONSORTIUM, SGC EXPDTA X-RAY DIFFRACTION AUTHOR R.NOWAK,T.KROJER,C.JOHANSSON,N.PEARCE,C.GILEADI,K.KUPINSKA,C.STRAIN- AUTHOR 2 DAMERELL,A.SZYKOWSKA,N.A.BURGESS-BROWN,C.H.ARROWSMITH,C.BOUNTRA, AUTHOR 3 A.M.EDWARDS,F.VON DELFT,P.E.BRENNAN,U.OPPERMANN REVDAT 3 10-JAN-24 5FYT 1 REMARK LINK REVDAT 2 24-JAN-18 5FYT 1 AUTHOR JRNL REVDAT 1 23-MAR-16 5FYT 0 JRNL AUTH R.NOWAK,T.KROJER,C.JOHANSSON,C.GILEADI,K.KUPINSKA, JRNL AUTH 2 C.STRAIN-DAMERELL,A.SZYKOWSKA,F.VON DELFT,N.A.BURGESS-BROWN, JRNL AUTH 3 C.H.ARROWSMITH,C.BOUNTRA,A.M.EDWARDS,U.OPPERMANN JRNL TITL CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B JRNL TITL 2 IN COMPLEX WITH N09996A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.87 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 74507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3808 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 70.9560 - 5.6092 1.00 2902 141 0.1747 0.1919 REMARK 3 2 5.6092 - 4.4524 1.00 2730 141 0.1402 0.1572 REMARK 3 3 4.4524 - 3.8896 1.00 2681 155 0.1399 0.1713 REMARK 3 4 3.8896 - 3.5340 1.00 2664 135 0.1554 0.2044 REMARK 3 5 3.5340 - 3.2807 1.00 2662 134 0.1778 0.2071 REMARK 3 6 3.2807 - 3.0873 1.00 2651 127 0.1912 0.2357 REMARK 3 7 3.0873 - 2.9327 1.00 2622 154 0.1947 0.2135 REMARK 3 8 2.9327 - 2.8050 1.00 2609 149 0.1964 0.2236 REMARK 3 9 2.8050 - 2.6970 1.00 2599 149 0.1956 0.2382 REMARK 3 10 2.6970 - 2.6039 1.00 2632 139 0.1961 0.2560 REMARK 3 11 2.6039 - 2.5225 1.00 2626 129 0.1984 0.2278 REMARK 3 12 2.5225 - 2.4504 1.00 2570 150 0.2018 0.2593 REMARK 3 13 2.4504 - 2.3859 1.00 2609 137 0.2096 0.2677 REMARK 3 14 2.3859 - 2.3277 1.00 2571 149 0.2086 0.2279 REMARK 3 15 2.3277 - 2.2748 1.00 2597 152 0.2210 0.2532 REMARK 3 16 2.2748 - 2.2264 1.00 2610 134 0.2343 0.2564 REMARK 3 17 2.2264 - 2.1818 1.00 2576 146 0.2350 0.2530 REMARK 3 18 2.1818 - 2.1406 1.00 2584 129 0.2286 0.2559 REMARK 3 19 2.1406 - 2.1024 1.00 2636 106 0.2445 0.2824 REMARK 3 20 2.1024 - 2.0668 1.00 2584 135 0.2521 0.2969 REMARK 3 21 2.0668 - 2.0334 1.00 2570 136 0.2588 0.3358 REMARK 3 22 2.0334 - 2.0021 1.00 2604 129 0.2682 0.3336 REMARK 3 23 2.0021 - 1.9727 1.00 2547 148 0.2745 0.3001 REMARK 3 24 1.9727 - 1.9449 1.00 2597 135 0.2850 0.3310 REMARK 3 25 1.9449 - 1.9186 1.00 2548 153 0.3099 0.3373 REMARK 3 26 1.9186 - 1.8937 1.00 2562 156 0.3015 0.3628 REMARK 3 27 1.8937 - 1.8700 1.00 2556 160 0.3100 0.3625 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.730 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3940 REMARK 3 ANGLE : 1.091 5329 REMARK 3 CHIRALITY : 0.047 561 REMARK 3 PLANARITY : 0.006 682 REMARK 3 DIHEDRAL : 14.633 1444 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: GLYCINE LINKER IS UNOBSERVED. REMARK 4 REMARK 4 5FYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1290066407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91732 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74577 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 95.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 19.600 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 20.20 REMARK 200 R MERGE FOR SHELL (I) : 1.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: DIMPLE REMARK 200 STARTING MODEL: PDB ENTRY 5A3P REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM REMARK 280 PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.22000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.61000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.91500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 25.30500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 126.52500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 101.22000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 50.61000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 25.30500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 75.91500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 126.52500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2309 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 102 REMARK 465 GLY A 103 REMARK 465 GLY A 104 REMARK 465 GLY A 105 REMARK 465 ALA A 374 REMARK 465 GLY A 443 REMARK 465 LYS A 444 REMARK 465 SER A 754 REMARK 465 TYR A 755 REMARK 465 ASN A 756 REMARK 465 GLU A 757 REMARK 465 TRP A 758 REMARK 465 ALA A 759 REMARK 465 LEU A 760 REMARK 465 ASN A 761 REMARK 465 VAL A 762 REMARK 465 ASN A 763 REMARK 465 GLU A 764 REMARK 465 ALA A 765 REMARK 465 LEU A 766 REMARK 465 GLU A 767 REMARK 465 ALA A 768 REMARK 465 LYS A 769 REMARK 465 ILE A 770 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 LYS A 100 CG CD CE NZ REMARK 470 LEU A 101 CG CD1 CD2 REMARK 470 ASP A 420 CG OD1 OD2 REMARK 470 LYS A 432 CG CD CE NZ REMARK 470 GLU A 433 CG CD OE1 OE2 REMARK 470 GLU A 450 CG CD OE1 OE2 REMARK 470 ASP A 478 CG OD1 OD2 REMARK 470 GLN A 545 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N04 WQS A 1757 O HOH A 2216 1.94 REMARK 500 OG SER A 470 O HOH A 2175 2.00 REMARK 500 OE1 GLU A 662 O2 EDO A 1769 2.04 REMARK 500 O HOH A 2042 O HOH A 2085 2.13 REMARK 500 OD1 ASP A 376 O HOH A 2062 2.13 REMARK 500 O HOH A 2193 O HOH A 2359 2.14 REMARK 500 O ILE A 417 O HOH A 2144 2.15 REMARK 500 O HOH A 2095 O HOH A 2359 2.15 REMARK 500 O HOH A 2324 O HOH A 2355 2.17 REMARK 500 O MET A 0 O HOH A 2001 2.18 REMARK 500 O1 EDO A 1774 O HOH A 2358 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2159 O HOH A 2209 9765 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 MET A 0 -72.98 56.20 REMARK 500 LEU A 90 76.47 -119.96 REMARK 500 VAL A 398 19.90 -61.33 REMARK 500 HIS A 399 -3.95 -168.88 REMARK 500 PHE A 493 -10.88 75.67 REMARK 500 PHE A 700 -53.78 -149.33 REMARK 500 LYS A 709 75.77 -114.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 VAL A 398 HIS A 399 -139.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1756 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 499 NE2 REMARK 620 2 GLU A 501 OE2 90.0 REMARK 620 3 HIS A 587 NE2 85.6 88.4 REMARK 620 4 WQS A1757 O14 96.4 173.6 91.6 REMARK 620 5 HOH A2196 O 84.0 88.9 169.2 92.2 REMARK 620 6 HOH A2201 O 173.6 90.2 100.8 83.5 89.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1754 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 692 SG REMARK 620 2 CYS A 695 SG 109.3 REMARK 620 3 CYS A 715 SG 116.8 111.7 REMARK 620 4 HIS A 718 ND1 109.8 107.0 101.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1755 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 706 SG REMARK 620 2 CYS A 708 SG 127.8 REMARK 620 3 CYS A 723 SG 103.9 107.2 REMARK 620 4 CYS A 725 SG 104.6 98.1 115.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1754 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1755 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 1756 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE WQS A 1757 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1758 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1759 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1760 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1761 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1762 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1763 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1764 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1765 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1766 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1767 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1780 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1768 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1769 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1770 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1771 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1772 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1773 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1774 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1775 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1776 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMS A 1777 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 1778 REMARK 800 REMARK 800 SITE_IDENTIFIER: CC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1779 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FXV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH N05859B REMARK 900 RELATED ID: 5FXW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FXX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH OXALOACETATE REMARK 900 RELATED ID: 5FXZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH CITRATE REMARK 900 RELATED ID: 5FY0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH L-MALATE REMARK 900 RELATED ID: 5FY1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH N08619B REMARK 900 RELATED ID: 5FY4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FY5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FY7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FY8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH D- THREO- REMARK 900 ISOCITRATE REMARK 900 RELATED ID: 5FY9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 5FYB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MC1648 REMARK 900 RELATED ID: 5FYC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH SUCCINATE REMARK 900 RELATED ID: 5FYH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH FUMARATE REMARK 900 RELATED ID: 5FYI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH PYRUVATE REMARK 900 RELATED ID: 5FYM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF JMJC DOMAIN OF HUMAN HISTONE DEMETHYLASE UTY REMARK 900 IN COMPLEX WITH D-2-HYDROXYGLUTARATE REMARK 900 RELATED ID: 5FYS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH D-2-HYDROXYGLUTARATE REMARK 900 RELATED ID: 5FYU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N10042A REMARK 900 RELATED ID: 5FYV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH OXALOACETATE REMARK 900 RELATED ID: 5FYY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N05798A REMARK 900 RELATED ID: 5FYZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N10063A REMARK 900 RELATED ID: 5FZ0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N11213A REMARK 900 RELATED ID: 5FZ1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH E48115B REMARK 900 RELATED ID: 5FZ3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N08776B REMARK 900 RELATED ID: 5FZ4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH N10057A REMARK 900 RELATED ID: 5FZ6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT N05859B ( LIGAND MODELLED BASED ON REMARK 900 PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZ7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT ETHYL 2- AMINO-4-THIOPHEN-2- REMARK 900 YLTHIOPHENE-3-CARBOXYLATE (N06131B ) (LIGAND MODELLED BASED ON REMARK 900 PANDDA EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZ8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MALATE REMARK 900 RELATED ID: 5FZ9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT THIENO(3,2 -B)THIOPHENE-5- REMARK 900 CARBOXYLIC ACID (N06263B) (LIGAND MODELLED BASED ON PANDDA EVENT REMARK 900 MAP, SGC - DIAMOND I04 -1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH 3D FRAGMENT 2-PIPERIDIN-4- YLOXY-5-(TRIFLUOROMETHYL) REMARK 900 PYRIDINE (N10072A) (LIGAND MODELLED BASED ON PANDDA EVENT MAP) REMARK 900 RELATED ID: 5FZB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT 4- PYRIDYLTHIOUREA (N06275B) REMARK 900 (LIGAND MODELLED BASED ON PANDDA EVENT MAP, SGC - DIAMOND I04-1 REMARK 900 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZC RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT 4,5- DIHYDRONAPHTHO(1,2-B)THIOPHENE- REMARK 900 2-CARBOXYLICACID (N11181A ) (LIGAND MODELLED BASED ON PANDDA EVENT REMARK 900 MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH L-2-HYDROXYGLUTARATE REMARK 900 RELATED ID: 5FZE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MC3960 REMARK 900 RELATED ID: 5FZF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MC3962 REMARK 900 RELATED ID: 5FZG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MC3948 REMARK 900 RELATED ID: 5FZH RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MAYBRIDGE FRAGMENT 4,5- DIHYDRONAPHTHO(1,2-B)THIOPHENE- REMARK 900 2-CARBOXYLICACID (N11181A ) (LIGAND MODELLED BASED ON PANDDA EVENT REMARK 900 MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH MC3095 REMARK 900 RELATED ID: 5FZK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH 3D FRAGMENT N,3-DIMETHYL-N -(PYRIDIN-3-YLMETHYL)-1,2- REMARK 900 OXAZOLE-5-CARBOXAMIDE ( N10051A) (LIGAND MODELLED BASED ON PANDDA REMARK 900 EVENT MAP, SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH 3D FRAGMENT 3-METHYL-N- PYRIDIN-4-YL-1,2-OXAZOLE-5- REMARK 900 CARBOXAMIDE (N09954A) ( LIGAND MODELLED BASED ON PANDDA EVENT MAP, REMARK 900 SGC - DIAMOND I04-1 FRAGMENT SCREENING) REMARK 900 RELATED ID: 5FZM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN JARID1B IN REMARK 900 COMPLEX WITH 3D FRAGMENT 5-(2-FLUOROPHENYL )-1,3-OXAZOLE-4- REMARK 900 CARBOXYLIC ACID (N09989B) (LIGAND MODELLED BASED ON PANDDA EVENT REMARK 900 MAP, SGC - DIAMOND I04 -1 FRAGMENT SCREENING) REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES S AND M COME FROM THE EXPRESSION VECTOR. RESIDUES REMARK 999 102-373 WERE DELETED FROM THE ORIGINAL SEQUENCE Q9UGL1. REMARK 999 DELETED RESIDUES WERE LINKED WITH 4 GLYCINE LINKER (GGGG). DBREF 5FYT A 26 101 UNP Q9UGL1 KDM5B_HUMAN 26 101 DBREF 5FYT A 374 770 UNP Q9UGL1 KDM5B_HUMAN 374 770 SEQADV 5FYT SER A -1 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FYT MET A 0 UNP Q9UGL1 EXPRESSION TAG SEQADV 5FYT GLY A 102 UNP Q9UGL1 LINKER SEQADV 5FYT GLY A 103 UNP Q9UGL1 LINKER SEQADV 5FYT GLY A 104 UNP Q9UGL1 LINKER SEQADV 5FYT GLY A 105 UNP Q9UGL1 LINKER SEQRES 1 A 479 SER MET PHE LEU PRO PRO PRO GLU CYS PRO VAL PHE GLU SEQRES 2 A 479 PRO SER TRP GLU GLU PHE ALA ASP PRO PHE ALA PHE ILE SEQRES 3 A 479 HIS LYS ILE ARG PRO ILE ALA GLU GLN THR GLY ILE CYS SEQRES 4 A 479 LYS VAL ARG PRO PRO PRO ASP TRP GLN PRO PRO PHE ALA SEQRES 5 A 479 CYS ASP VAL ASP LYS LEU HIS PHE THR PRO ARG ILE GLN SEQRES 6 A 479 ARG LEU ASN GLU LEU GLU ALA GLN THR ARG VAL LYS LEU SEQRES 7 A 479 GLY GLY GLY GLY ALA ARG ASP TYR THR LEU ARG THR PHE SEQRES 8 A 479 GLY GLU MET ALA ASP ALA PHE LYS SER ASP TYR PHE ASN SEQRES 9 A 479 MET PRO VAL HIS MET VAL PRO THR GLU LEU VAL GLU LYS SEQRES 10 A 479 GLU PHE TRP ARG LEU VAL SER THR ILE GLU GLU ASP VAL SEQRES 11 A 479 THR VAL GLU TYR GLY ALA ASP ILE ALA SER LYS GLU PHE SEQRES 12 A 479 GLY SER GLY PHE PRO VAL ARG ASP GLY LYS ILE LYS LEU SEQRES 13 A 479 SER PRO GLU GLU GLU GLU TYR LEU ASP SER GLY TRP ASN SEQRES 14 A 479 LEU ASN ASN MET PRO VAL MET GLU GLN SER VAL LEU ALA SEQRES 15 A 479 HIS ILE THR ALA ASP ILE CYS GLY MET LYS LEU PRO TRP SEQRES 16 A 479 LEU TYR VAL GLY MET CYS PHE SER SER PHE CYS TRP HIS SEQRES 17 A 479 ILE GLU ASP HIS TRP SER TYR SER ILE ASN TYR LEU HIS SEQRES 18 A 479 TRP GLY GLU PRO LYS THR TRP TYR GLY VAL PRO GLY TYR SEQRES 19 A 479 ALA ALA GLU GLN LEU GLU ASN VAL MET LYS LYS LEU ALA SEQRES 20 A 479 PRO GLU LEU PHE VAL SER GLN PRO ASP LEU LEU HIS GLN SEQRES 21 A 479 LEU VAL THR ILE MET ASN PRO ASN THR LEU MET THR HIS SEQRES 22 A 479 GLU VAL PRO VAL TYR ARG THR ASN GLN CYS ALA GLY GLU SEQRES 23 A 479 PHE VAL ILE THR PHE PRO ARG ALA TYR HIS SER GLY PHE SEQRES 24 A 479 ASN GLN GLY PHE ASN PHE ALA GLU ALA VAL ASN PHE CYS SEQRES 25 A 479 THR VAL ASP TRP LEU PRO LEU GLY ARG GLN CYS VAL GLU SEQRES 26 A 479 HIS TYR ARG LEU LEU HIS ARG TYR CYS VAL PHE SER HIS SEQRES 27 A 479 ASP GLU MET ILE CYS LYS MET ALA SER LYS ALA ASP VAL SEQRES 28 A 479 LEU ASP VAL VAL VAL ALA SER THR VAL GLN LYS ASP MET SEQRES 29 A 479 ALA ILE MET ILE GLU ASP GLU LYS ALA LEU ARG GLU THR SEQRES 30 A 479 VAL ARG LYS LEU GLY VAL ILE ASP SER GLU ARG MET ASP SEQRES 31 A 479 PHE GLU LEU LEU PRO ASP ASP GLU ARG GLN CYS VAL LYS SEQRES 32 A 479 CYS LYS THR THR CYS PHE MET SER ALA ILE SER CYS SER SEQRES 33 A 479 CYS LYS PRO GLY LEU LEU VAL CYS LEU HIS HIS VAL LYS SEQRES 34 A 479 GLU LEU CYS SER CYS PRO PRO TYR LYS TYR LYS LEU ARG SEQRES 35 A 479 TYR ARG TYR THR LEU ASP ASP LEU TYR PRO MET MET ASN SEQRES 36 A 479 ALA LEU LYS LEU ARG ALA GLU SER TYR ASN GLU TRP ALA SEQRES 37 A 479 LEU ASN VAL ASN GLU ALA LEU GLU ALA LYS ILE HET ZN A1754 1 HET ZN A1755 1 HET MN A1756 1 HET WQS A1757 15 HET EDO A1758 4 HET EDO A1759 4 HET EDO A1760 4 HET EDO A1761 4 HET EDO A1762 4 HET EDO A1763 4 HET EDO A1764 4 HET EDO A1765 4 HET EDO A1766 4 HET EDO A1767 4 HET EDO A1768 4 HET EDO A1769 4 HET EDO A1770 4 HET EDO A1771 4 HET EDO A1772 4 HET EDO A1773 4 HET EDO A1774 4 HET DMS A1775 4 HET DMS A1776 4 HET DMS A1777 4 HET PO4 A1778 5 HET CL A1779 1 HET EDO A1780 4 HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM WQS 2-[(3S)-5-FLUORANYL-2-OXIDANYLIDENE-1,3-DIHYDROINDOL-3- HETNAM 2 WQS YL]ETHANOIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETNAM PO4 PHOSPHATE ION HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN 2(ZN 2+) FORMUL 4 MN MN 2+ FORMUL 5 WQS C10 H8 F N O3 FORMUL 6 EDO 18(C2 H6 O2) FORMUL 23 DMS 3(C2 H6 O S) FORMUL 26 PO4 O4 P 3- FORMUL 27 CL CL 1- FORMUL 29 HOH *360(H2 O) HELIX 1 1 SER A 38 ASP A 44 1 7 HELIX 2 2 ASP A 44 GLU A 57 1 14 HELIX 3 3 LEU A 379 ASN A 395 1 17 HELIX 4 4 PRO A 402 THR A 416 1 15 HELIX 5 5 SER A 448 LEU A 455 1 8 HELIX 6 6 SER A 470 HIS A 474 5 5 HELIX 7 7 ILE A 479 LEU A 484 1 6 HELIX 8 8 GLU A 501 SER A 505 5 5 HELIX 9 9 PRO A 523 TYR A 525 5 3 HELIX 10 10 ALA A 526 ALA A 538 1 13 HELIX 11 11 PRO A 539 VAL A 543 5 5 HELIX 12 12 ASN A 557 HIS A 564 1 8 HELIX 13 13 THR A 604 ASP A 606 5 3 HELIX 14 14 TRP A 607 HIS A 622 1 16 HELIX 15 15 SER A 628 SER A 638 1 11 HELIX 16 16 LYS A 639 LEU A 643 5 5 HELIX 17 17 ASP A 644 LEU A 672 1 29 HELIX 18 18 ASP A 681 LEU A 685 5 5 HELIX 19 19 PRO A 686 ARG A 690 5 5 HELIX 20 20 HIS A 718 LEU A 722 5 5 HELIX 21 21 PRO A 726 TYR A 728 5 3 HELIX 22 22 THR A 737 GLU A 753 1 17 SHEET 1 AA 7 VAL A 34 PHE A 35 0 SHEET 2 AA 7 ILE A 61 VAL A 64 1 O LYS A 63 N PHE A 35 SHEET 3 AA 7 PHE A 578 THR A 581 -1 O PHE A 578 N VAL A 64 SHEET 4 AA 7 TYR A 506 GLY A 514 -1 O SER A 507 N THR A 581 SHEET 5 AA 7 ASN A 595 PHE A 602 -1 O PHE A 596 N HIS A 512 SHEET 6 AA 7 TRP A 486 GLY A 490 -1 O TRP A 486 N ALA A 599 SHEET 7 AA 7 ASP A 428 ILE A 429 -1 O ASP A 428 N LEU A 487 SHEET 1 AB 2 HIS A 82 PHE A 83 0 SHEET 2 AB 2 TYR A 377 THR A 378 -1 O TYR A 377 N PHE A 83 SHEET 1 AC 2 ARG A 86 ARG A 89 0 SHEET 2 AC 2 THR A 422 TYR A 425 -1 O VAL A 423 N GLN A 88 SHEET 1 AD 2 GLN A 96 THR A 97 0 SHEET 2 AD 2 LEU A 552 VAL A 553 -1 O VAL A 553 N GLN A 96 SHEET 1 AE 4 SER A 495 HIS A 499 0 SHEET 2 AE 4 HIS A 587 ASN A 591 -1 O HIS A 587 N HIS A 499 SHEET 3 AE 4 LYS A 517 GLY A 521 -1 O THR A 518 N PHE A 590 SHEET 4 AE 4 TYR A 569 GLN A 573 -1 O TYR A 569 N GLY A 521 SHEET 1 AF 3 ASP A 676 ARG A 679 0 SHEET 2 AF 3 TYR A 730 TYR A 734 1 O TYR A 730 N ASP A 676 SHEET 3 AF 3 SER A 702 CYS A 706 -1 O ALA A 703 N ARG A 733 LINK NE2 HIS A 499 MN MN A1756 1555 1555 2.12 LINK OE2 GLU A 501 MN MN A1756 1555 1555 2.06 LINK NE2 HIS A 587 MN MN A1756 1555 1555 2.14 LINK SG CYS A 692 ZN ZN A1754 1555 1555 2.15 LINK SG CYS A 695 ZN ZN A1754 1555 1555 2.39 LINK SG CYS A 706 ZN ZN A1755 1555 1555 2.48 LINK SG CYS A 708 ZN ZN A1755 1555 1555 2.53 LINK SG CYS A 715 ZN ZN A1754 1555 1555 2.28 LINK ND1 HIS A 718 ZN ZN A1754 1555 1555 2.13 LINK SG CYS A 723 ZN ZN A1755 1555 1555 2.36 LINK SG CYS A 725 ZN ZN A1755 1555 1555 2.72 LINK MN MN A1756 O14 WQS A1757 1555 1555 2.17 LINK MN MN A1756 O HOH A2196 1555 1555 2.08 LINK MN MN A1756 O HOH A2201 1555 1555 2.18 SITE 1 AC1 4 CYS A 692 CYS A 695 CYS A 715 HIS A 718 SITE 1 AC2 4 CYS A 706 CYS A 708 CYS A 723 CYS A 725 SITE 1 AC3 6 HIS A 499 GLU A 501 HIS A 587 WQS A1757 SITE 2 AC3 6 HOH A2196 HOH A2201 SITE 1 AC4 15 TYR A 488 PHE A 496 HIS A 499 ASN A 509 SITE 2 AC4 15 LYS A 517 TRP A 519 HIS A 587 MN A1756 SITE 3 AC4 15 DMS A1776 HOH A2090 HOH A2093 HOH A2095 SITE 4 AC4 15 HOH A2196 HOH A2201 HOH A2216 SITE 1 AC5 7 PHE A 83 GLY A 426 ALA A 427 LEU A 487 SITE 2 AC5 7 TYR A 488 VAL A 489 HOH A2154 SITE 1 AC6 5 ARG A 666 LEU A 732 TYR A 734 HOH A2289 SITE 2 AC6 5 HOH A2348 SITE 1 AC7 4 ARG A 612 ASP A 630 MET A 658 GLU A 662 SITE 1 AC8 2 PRO A 30 VAL A 568 SITE 1 AC9 9 ASP A 688 GLU A 689 ARG A 690 GLN A 691 SITE 2 AC9 9 VAL A 693 GLY A 711 LEU A 712 LEU A 713 SITE 3 AC9 9 HOH A2350 SITE 1 BC1 7 GLY A 524 TYR A 525 ARG A 584 LEU A 610 SITE 2 BC1 7 HOH A2218 HOH A2351 HOH A2352 SITE 1 BC2 5 ARG A 670 VAL A 674 ILE A 675 HOH A2145 SITE 2 BC2 5 HOH A2288 SITE 1 BC3 5 ASP A 387 ALA A 388 VAL A 398 HOH A2107 SITE 2 BC3 5 HOH A2114 SITE 1 BC4 5 LEU A 405 LYS A 408 GLU A 409 ASP A 676 SITE 2 BC4 5 HOH A2141 SITE 1 BC5 4 GLU A 678 LYS A 731 ARG A 733 HOH A2354 SITE 1 BC6 1 HOH A2360 SITE 1 BC7 5 LEU A 27 PRO A 28 PRO A 29 MET A 562 SITE 2 BC7 5 LEU A 750 SITE 1 BC8 8 GLU A 662 LEU A 665 MET A 701 SER A 702 SITE 2 BC8 8 CYS A 715 LEU A 716 HOH A2334 HOH A2355 SITE 1 BC9 4 LYS A 80 GLU A 721 CYS A 723 SER A 724 SITE 1 CC1 3 TRP A 39 GLU A 453 HOH A2047 SITE 1 CC2 2 ARG A 679 HOH A2306 SITE 1 CC3 5 TRP A 504 HIS A 617 TYR A 618 HOH A2227 SITE 2 CC3 5 HOH A2356 SITE 1 CC4 5 LEU A 716 HIS A 717 VAL A 719 HOH A2332 SITE 2 CC4 5 HOH A2358 SITE 1 CC5 4 GLU A 631 LYS A 635 GLU A 683 TYR A 736 SITE 1 CC6 8 GLN A 88 THR A 97 TYR A 425 SER A 495 SITE 2 CC6 8 PHE A 496 CYS A 497 WQS A1757 HOH A2193 SITE 1 CC7 6 TRP A 486 TYR A 488 GLU A 501 VAL A 600 SITE 2 CC7 6 ASN A 601 HOH A2196 SITE 1 CC8 5 HIS A 622 LYS A 694 HIS A 718 HOH A2255 SITE 2 CC8 5 HOH A2259 SITE 1 CC9 5 LEU A 90 ASN A 91 LEU A 413 THR A 416 SITE 2 CC9 5 GLU A 419 CRYST1 141.810 141.810 151.830 90.00 90.00 120.00 P 65 2 2 12 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007052 0.004071 0.000000 0.00000 SCALE2 0.000000 0.008143 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006586 0.00000