PDB Short entry for 3U78 HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 13-OCT-11 3U78 TITLE E67-2 SELECTIVELY INHIBITS KIAA1718, A HUMAN HISTONE H3 LYSINE 9 TITLE 2 JUMONJI DEMETHYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JUMONJI DOMAIN (UNP RESIDUES 92-488); COMPND 5 SYNONYM: KIAA1718, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION COMPND 6 PROTEIN 1D; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: JHDM1D, KDM7, KIAA1718; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EPIGENETICS, HISTONE LYSINE DEMETHYLATION, BIX ANALOGS, KEYWDS 2 OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.K.UPADHYAY,X.CHENG REVDAT 3 13-SEP-23 3U78 1 REMARK LINK REVDAT 2 22-FEB-12 3U78 1 JRNL REVDAT 1 25-JAN-12 3U78 0 JRNL AUTH A.K.UPADHYAY,D.ROTILI,J.W.HAN,R.HU,Y.CHANG,D.LABELLA, JRNL AUTH 2 X.ZHANG,Y.S.YOON,A.MAI,X.CHENG JRNL TITL AN ANALOG OF BIX-01294 SELECTIVELY INHIBITS A FAMILY OF JRNL TITL 2 HISTONE H3 LYSINE 9 JUMONJI DEMETHYLASES. JRNL REF J.MOL.BIOL. V. 416 319 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22227394 JRNL DOI 10.1016/J.JMB.2011.12.036 REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_336) 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) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.080 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 14472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1448 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 26.5943 - 5.7764 0.98 1508 168 0.2007 0.2354 REMARK 3 2 5.7764 - 4.5926 0.98 1378 154 0.1612 0.2213 REMARK 3 3 4.5926 - 4.0143 0.99 1361 151 0.1583 0.2097 REMARK 3 4 4.0143 - 3.6483 0.99 1351 149 0.1891 0.2853 REMARK 3 5 3.6483 - 3.3873 0.98 1316 147 0.1912 0.2883 REMARK 3 6 3.3873 - 3.1880 0.96 1286 143 0.2186 0.2823 REMARK 3 7 3.1880 - 3.0286 0.95 1275 142 0.2126 0.2912 REMARK 3 8 3.0286 - 2.8969 0.92 1227 136 0.2287 0.3013 REMARK 3 9 2.8969 - 2.7855 0.91 1186 132 0.2380 0.3598 REMARK 3 10 2.7855 - 2.6890 0.86 1136 126 0.2136 0.2919 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 : 0.32 REMARK 3 B_SOL : 41.32 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 48.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.01840 REMARK 3 B22 (A**2) : 8.01840 REMARK 3 B33 (A**2) : -16.03680 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.008 3067 REMARK 3 ANGLE : 1.195 4156 REMARK 3 CHIRALITY : 0.080 451 REMARK 3 PLANARITY : 0.006 523 REMARK 3 DIHEDRAL : 16.359 1125 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: NULL REMARK 4 REMARK 4 3U78 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068393. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK DOUBLE-CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14476 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.689 REMARK 200 RESOLUTION RANGE LOW (A) : 26.593 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 18.70 REMARK 200 R MERGE (I) : 0.12400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.40 REMARK 200 R MERGE FOR SHELL (I) : 0.70800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 3KVA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-20% V/V PEG5000 MME, 0.2 M CALCIUM REMARK 280 CHLORIDE, 0.1 M BIS-TRIS, PH 6.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 96.56167 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 193.12333 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 144.84250 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 241.40417 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 48.28083 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 96.56167 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 193.12333 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 241.40417 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 144.84250 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 48.28083 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 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 A 809 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 SER A 92 REMARK 465 LEU A 93 REMARK 465 MET A 94 REMARK 465 LYS A 95 REMARK 465 LYS A 96 REMARK 465 ARG A 97 REMARK 465 ARG A 98 REMARK 465 ASN A 99 REMARK 465 TRP A 100 REMARK 465 HIS A 101 REMARK 465 ARG A 102 REMARK 465 HIS A 103 REMARK 465 ASP A 104 REMARK 465 TYR A 105 REMARK 465 THR A 106 REMARK 465 GLU A 107 REMARK 465 ILE A 108 REMARK 465 ASP A 109 REMARK 465 ASP A 110 REMARK 465 GLY A 111 REMARK 465 SER A 112 REMARK 465 LYS A 113 REMARK 465 GLY A 480 REMARK 465 LYS A 481 REMARK 465 PRO A 482 REMARK 465 VAL A 483 REMARK 465 LYS A 484 REMARK 465 SER A 485 REMARK 465 GLN A 486 REMARK 465 GLY A 487 REMARK 465 ILE A 488 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 LYS A 124 CG CD CE NZ REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 GLU A 240 CG CD OE1 OE2 REMARK 470 PHE A 394 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG A 418 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 445 CG CD CE NZ REMARK 470 LYS A 466 CG CD CE NZ REMARK 470 SER A 469 OG REMARK 470 ARG A 473 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 477 CG CD OE1 OE2 REMARK 470 GLU A 478 CG CD OE1 OE2 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 PRO A 173 155.58 -46.72 REMARK 500 PRO A 175 1.56 -57.58 REMARK 500 PRO A 217 -166.49 -67.83 REMARK 500 VAL A 266 30.22 -146.81 REMARK 500 ASP A 276 3.84 81.49 REMARK 500 PHE A 398 41.71 -109.00 REMARK 500 ALA A 474 155.78 77.23 REMARK 500 ILE A 475 -59.83 74.19 REMARK 500 GLU A 477 -60.93 87.83 REMARK 500 GLU A 478 4.87 -64.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 E67 A 707 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 NI A 702 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 282 NE2 REMARK 620 2 ASP A 284 OD1 95.7 REMARK 620 3 HIS A 354 NE2 87.7 94.3 REMARK 620 4 AKG A 701 O5 89.3 174.2 89.0 REMARK 620 5 AKG A 701 O1 94.4 96.5 168.7 79.9 REMARK 620 6 HOH A 801 O 176.9 87.1 90.7 88.1 86.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE E67 A 707 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KVA RELATED DB: PDB REMARK 900 STRUCTURE OF KIAA1718 JUMONJI DOMAIN IN COMPLEX WITH ALPHA- REMARK 900 KETOGLUTARATE DBREF 3U78 A 92 488 UNP Q6ZMT4 KDM7_HUMAN 92 488 SEQRES 1 A 397 SER LEU MET LYS LYS ARG ARG ASN TRP HIS ARG HIS ASP SEQRES 2 A 397 TYR THR GLU ILE ASP ASP GLY SER LYS PRO VAL GLN ALA SEQRES 3 A 397 GLY THR ARG THR PHE ILE LYS GLU LEU ARG SER ARG VAL SEQRES 4 A 397 PHE PRO SER ALA ASP GLU ILE ILE ILE LYS MET HIS GLY SEQRES 5 A 397 SER GLN LEU THR GLN ARG TYR LEU GLU LYS HIS GLY PHE SEQRES 6 A 397 ASP VAL PRO ILE MET VAL PRO LYS LEU ASP ASP LEU GLY SEQRES 7 A 397 LEU ARG LEU PRO SER PRO THR PHE SER VAL MET ASP VAL SEQRES 8 A 397 GLU ARG TYR VAL GLY GLY ASP LYS VAL ILE ASP VAL ILE SEQRES 9 A 397 ASP VAL ALA ARG GLN ALA ASP SER LYS MET THR LEU HIS SEQRES 10 A 397 ASN TYR VAL LYS TYR PHE MET ASN PRO ASN ARG PRO LYS SEQRES 11 A 397 VAL LEU ASN VAL ILE SER LEU GLU PHE SER ASP THR LYS SEQRES 12 A 397 MET SER GLU LEU VAL GLU VAL PRO ASP ILE ALA LYS LYS SEQRES 13 A 397 LEU SER TRP VAL GLU ASN TYR TRP PRO ASP ASP SER VAL SEQRES 14 A 397 PHE PRO LYS PRO PHE VAL GLN LYS TYR CYS LEU MET GLY SEQRES 15 A 397 VAL GLN ASP SER TYR THR ASP PHE HIS ILE ASP PHE GLY SEQRES 16 A 397 GLY THR SER VAL TRP TYR HIS VAL LEU TRP GLY GLU LYS SEQRES 17 A 397 ILE PHE TYR LEU ILE LYS PRO THR ASP GLU ASN LEU ALA SEQRES 18 A 397 ARG TYR GLU SER TRP SER SER SER VAL THR GLN SER GLU SEQRES 19 A 397 VAL PHE PHE GLY ASP LYS VAL ASP LYS CYS TYR LYS CYS SEQRES 20 A 397 VAL VAL LYS GLN GLY HIS THR LEU PHE VAL PRO THR GLY SEQRES 21 A 397 TRP ILE HIS ALA VAL LEU THR SER GLN ASP CYS MET ALA SEQRES 22 A 397 PHE GLY GLY ASN PHE LEU HIS ASN LEU ASN ILE GLY MET SEQRES 23 A 397 GLN LEU ARG CYS TYR GLU MET GLU LYS ARG LEU LYS THR SEQRES 24 A 397 PRO ASP LEU PHE LYS PHE PRO PHE PHE GLU ALA ILE CYS SEQRES 25 A 397 TRP PHE VAL ALA LYS ASN LEU LEU GLU THR LEU LYS GLU SEQRES 26 A 397 LEU ARG GLU ASP GLY PHE GLN PRO GLN THR TYR LEU VAL SEQRES 27 A 397 GLN GLY VAL LYS ALA LEU HIS THR ALA LEU LYS LEU TRP SEQRES 28 A 397 MET LYS LYS GLU LEU VAL SER GLU HIS ALA PHE GLU ILE SEQRES 29 A 397 PRO ASP ASN VAL ARG PRO GLY HIS LEU ILE LYS GLU LEU SEQRES 30 A 397 SER LYS VAL ILE ARG ALA ILE GLU GLU GLU ASN GLY LYS SEQRES 31 A 397 PRO VAL LYS SER GLN GLY ILE HET AKG A 701 10 HET NI A 702 1 HET CL A 703 1 HET SO4 A 704 5 HET EDO A 705 4 HET EDO A 706 4 HET E67 A 707 27 HETNAM AKG 2-OXOGLUTARIC ACID HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM E67 7-[(5-AMINOPENTYL)OXY]-N~4~-(1-BENZYLPIPERIDIN-4-YL)- HETNAM 2 E67 N~2~-[3-(DIMETHYLAMINO)PROPYL]-6-METHOXYQUINAZOLINE-2, HETNAM 3 E67 4-DIAMINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 AKG C5 H6 O5 FORMUL 3 NI NI 2+ FORMUL 4 CL CL 1- FORMUL 5 SO4 O4 S 2- FORMUL 6 EDO 2(C2 H6 O2) FORMUL 8 E67 C31 H47 N7 O2 FORMUL 9 HOH *45(H2 O) HELIX 1 1 THR A 119 ARG A 129 1 11 HELIX 2 2 SER A 133 ILE A 137 5 5 HELIX 3 3 HIS A 142 LEU A 146 5 5 HELIX 4 4 THR A 147 GLY A 155 1 9 HELIX 5 5 SER A 178 GLY A 187 1 10 HELIX 6 6 LEU A 207 ASN A 216 1 10 HELIX 7 7 THR A 233 VAL A 239 5 7 HELIX 8 8 PRO A 242 SER A 249 1 8 HELIX 9 9 SER A 249 TRP A 255 1 7 HELIX 10 10 ASP A 284 THR A 288 5 5 HELIX 11 11 THR A 307 SER A 319 1 13 HELIX 12 12 THR A 322 VAL A 326 5 5 HELIX 13 13 PHE A 327 VAL A 332 5 6 HELIX 14 14 ASN A 374 LEU A 388 1 15 HELIX 15 15 THR A 390 PHE A 396 5 7 HELIX 16 16 PHE A 398 GLU A 419 1 22 HELIX 17 17 GLN A 425 LYS A 444 1 20 HELIX 18 18 LEU A 447 ILE A 455 5 9 HELIX 19 19 ARG A 460 ARG A 473 1 14 SHEET 1 A 6 ILE A 139 LYS A 140 0 SHEET 2 A 6 ILE A 160 VAL A 162 1 O MET A 161 N ILE A 139 SHEET 3 A 6 THR A 345 VAL A 348 -1 O THR A 345 N VAL A 162 SHEET 4 A 6 SER A 289 ILE A 304 -1 N TYR A 292 O LEU A 346 SHEET 5 A 6 ILE A 353 PHE A 369 -1 O PHE A 365 N HIS A 293 SHEET 6 A 6 SER A 277 HIS A 282 -1 N SER A 277 O THR A 358 SHEET 1 B 7 ALA A 201 THR A 206 0 SHEET 2 B 7 VAL A 191 ASP A 196 -1 N VAL A 194 O SER A 203 SHEET 3 B 7 LEU A 223 GLU A 229 -1 O ASN A 224 N ILE A 195 SHEET 4 B 7 TYR A 269 GLY A 273 -1 O MET A 272 N VAL A 225 SHEET 5 B 7 ILE A 353 PHE A 369 -1 O GLY A 366 N TYR A 269 SHEET 6 B 7 SER A 289 ILE A 304 -1 N HIS A 293 O PHE A 365 SHEET 7 B 7 TYR A 336 LYS A 341 -1 O CYS A 338 N PHE A 301 LINK NE2 HIS A 282 NI NI A 702 1555 1555 2.25 LINK OD1 ASP A 284 NI NI A 702 1555 1555 2.26 LINK NE2 HIS A 354 NI NI A 702 1555 1555 2.33 LINK O5 AKG A 701 NI NI A 702 1555 1555 2.19 LINK O1 AKG A 701 NI NI A 702 1555 1555 2.25 LINK NI NI A 702 O HOH A 801 1555 1555 2.27 SITE 1 AC1 13 ASN A 224 ILE A 226 THR A 279 HIS A 282 SITE 2 AC1 13 ASP A 284 TYR A 292 LYS A 299 HIS A 354 SITE 3 AC1 13 VAL A 356 NI A 702 E67 A 707 HOH A 801 SITE 4 AC1 13 HOH A 843 SITE 1 AC2 5 HIS A 282 ASP A 284 HIS A 354 AKG A 701 SITE 2 AC2 5 HOH A 801 SITE 1 AC3 5 SER A 249 TRP A 250 VAL A 251 PHE A 369 SITE 2 AC3 5 LEU A 370 SITE 1 AC4 3 GLU A 309 ARG A 313 ASP A 333 SITE 1 AC5 2 LYS A 153 HOH A 873 SITE 1 AC6 1 ASP A 167 SITE 1 AC7 9 GLN A 200 ASP A 202 LYS A 204 ASP A 280 SITE 2 AC7 9 ASP A 284 PHE A 285 PRO A 391 ASP A 392 SITE 3 AC7 9 AKG A 701 CRYST1 77.429 77.429 289.685 90.00 90.00 120.00 P 61 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 0.012915 0.007457 0.000000 0.00000 SCALE2 0.000000 0.014913 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003452 0.00000