PDB Short entry for 6FUL HEADER OXIDOREDUCTASE 27-FEB-18 6FUL TITLE CRYSTAL STRUCTURE OF UTX COMPLEXED WITH 5-HYDROXY-4-KETO-1-METHYL- TITLE 2 PICOLINATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 6A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE DEMETHYLASE UTX,UBIQUITOUSLY-TRANSCRIBED TPR PROTEIN COMPND 5 ON THE X CHROMOSOME,UBIQUITOUSLY-TRANSCRIBED X CHROMOSOME COMPND 6 TETRATRICOPEPTIDE REPEAT PROTEIN; 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: KDM6A, UTX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS JUMONJI DEMETHYLASE, INHIBITOR, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.ESPOSITO,P.SLEDZ,A.CAFLISCH REVDAT 3 17-JAN-24 6FUL 1 REMARK REVDAT 2 31-OCT-18 6FUL 1 COMPND JRNL REVDAT 1 10-OCT-18 6FUL 0 JRNL AUTH C.ESPOSITO,L.WIEDMER,A.CAFLISCH JRNL TITL IN SILICO IDENTIFICATION OF JMJD3 DEMETHYLASE INHIBITORS. JRNL REF J CHEM INF MODEL V. 58 2151 2018 JRNL REFN ESSN 1549-960X JRNL PMID 30226987 JRNL DOI 10.1021/ACS.JCIM.8B00539 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.200 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 138111 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.970 REMARK 3 FREE R VALUE TEST SET COUNT : 6862 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 48.7821 - 5.1223 0.98 4411 234 0.1718 0.1730 REMARK 3 2 5.1223 - 4.0664 0.94 4235 216 0.1318 0.1636 REMARK 3 3 4.0664 - 3.5525 0.97 4399 225 0.1446 0.1729 REMARK 3 4 3.5525 - 3.2278 0.98 4419 230 0.1585 0.1891 REMARK 3 5 3.2278 - 2.9965 0.98 4437 232 0.1700 0.1964 REMARK 3 6 2.9965 - 2.8198 0.98 4425 240 0.1686 0.1993 REMARK 3 7 2.8198 - 2.6786 0.97 4388 229 0.1712 0.2096 REMARK 3 8 2.6786 - 2.5620 0.96 4342 225 0.1816 0.2363 REMARK 3 9 2.5620 - 2.4634 0.95 4260 231 0.1844 0.2091 REMARK 3 10 2.4634 - 2.3784 0.94 4221 217 0.1753 0.2467 REMARK 3 11 2.3784 - 2.3040 0.97 4369 226 0.1775 0.2244 REMARK 3 12 2.3040 - 2.2382 0.97 4379 229 0.1790 0.2312 REMARK 3 13 2.2382 - 2.1793 0.98 4449 230 0.1760 0.2163 REMARK 3 14 2.1793 - 2.1261 0.98 4396 229 0.1809 0.2370 REMARK 3 15 2.1261 - 2.0778 0.99 4446 230 0.1807 0.2080 REMARK 3 16 2.0778 - 2.0335 0.99 4509 237 0.1884 0.2290 REMARK 3 17 2.0335 - 1.9929 0.99 4470 231 0.1895 0.2208 REMARK 3 18 1.9929 - 1.9553 0.99 4493 237 0.1969 0.2388 REMARK 3 19 1.9553 - 1.9203 0.99 4446 237 0.2007 0.2280 REMARK 3 20 1.9203 - 1.8878 0.98 4408 232 0.2084 0.2361 REMARK 3 21 1.8878 - 1.8573 0.97 4374 230 0.2229 0.2702 REMARK 3 22 1.8573 - 1.8288 0.97 4365 230 0.2340 0.2825 REMARK 3 23 1.8288 - 1.8019 0.95 4290 222 0.2392 0.2572 REMARK 3 24 1.8019 - 1.7765 0.96 4360 232 0.2446 0.2879 REMARK 3 25 1.7765 - 1.7525 0.96 4324 226 0.2586 0.3055 REMARK 3 26 1.7525 - 1.7297 0.96 4326 225 0.2699 0.2877 REMARK 3 27 1.7297 - 1.7081 0.97 4401 233 0.2827 0.2696 REMARK 3 28 1.7081 - 1.6875 0.98 4379 222 0.2922 0.3254 REMARK 3 29 1.6875 - 1.6679 0.98 4477 230 0.3045 0.3280 REMARK 3 30 1.6679 - 1.6491 0.89 4051 215 0.3376 0.3553 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 4045 REMARK 3 ANGLE : 0.803 5513 REMARK 3 CHIRALITY : 0.054 596 REMARK 3 PLANARITY : 0.006 710 REMARK 3 DIHEDRAL : 3.955 3289 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 6FUL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1200008116. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999990 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 138199 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.649 REMARK 200 RESOLUTION RANGE LOW (A) : 48.761 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 1.960 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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: 3AVS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL (PH 8.5), LI2 SO4 (0.15 REMARK 280 -0.25 M), PEG 3350 (20-25% W/V), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 39.59050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.57800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.40050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.57800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.59050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.40050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 1390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22820 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 KCAL/MOL 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 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 871 REMARK 465 PRO A 872 REMARK 465 GLY A 873 REMARK 465 TYR A 874 REMARK 465 GLN A 875 REMARK 465 ASP A 876 REMARK 465 PRO A 877 REMARK 465 ASN A 878 REMARK 465 SER A 879 REMARK 465 GLN A 880 REMARK 465 ILE A 881 REMARK 465 ILE A 882 REMARK 465 PRO A 883 REMARK 465 SER A 884 REMARK 465 MET A 885 REMARK 465 LEU A 903 REMARK 465 GLY A 904 REMARK 465 LYS A 905 REMARK 465 ASN A 906 REMARK 465 GLY A 907 REMARK 465 ASN A 1051 REMARK 465 GLU A 1052 REMARK 465 LYS A 1053 REMARK 465 ARG A 1054 REMARK 465 SER A 1055 REMARK 465 HIS A 1056 REMARK 465 HIS A 1057 REMARK 465 LYS A 1058 REMARK 465 ASP A 1059 REMARK 465 HIS A 1060 REMARK 465 SER A 1061 REMARK 465 ASP A 1062 REMARK 465 SER A 1063 REMARK 465 GLU A 1064 REMARK 465 SER A 1065 REMARK 465 THR A 1066 REMARK 465 SER A 1067 REMARK 465 SER A 1068 REMARK 465 ASP A 1069 REMARK 465 ASN A 1070 REMARK 465 SER A 1071 REMARK 465 GLY A 1072 REMARK 465 ARG A 1073 REMARK 465 ARG A 1074 REMARK 465 ARG A 1075 REMARK 465 LYS A 1076 REMARK 465 GLY A 1077 REMARK 465 LEU A 1396 REMARK 465 PRO A 1397 REMARK 465 SER A 1398 REMARK 465 ALA A 1399 REMARK 465 SER A 1400 REMARK 465 SER A 1401 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 ARG A 901 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 902 CG OD1 ND2 REMARK 470 LEU A 908 CG CD1 CD2 REMARK 470 ARG A1048 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1049 CG CD OE1 OE2 REMARK 470 GLU A1050 CG CD OE1 OE2 REMARK 470 LYS A1183 CG CD CE NZ REMARK 470 GLN A1304 CG CD OE1 NE2 REMARK 470 LYS A1324 CG CD CE NZ REMARK 470 GLU A1370 OE1 OE2 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 O HOH A 1612 O HOH A 1728 1.98 REMARK 500 O HOH A 1884 O HOH A 2053 2.02 REMARK 500 O HOH A 2103 O HOH A 2106 2.05 REMARK 500 O HOH A 1932 O HOH A 2105 2.12 REMARK 500 O HOH A 1863 O HOH A 2111 2.13 REMARK 500 O HOH A 2045 O HOH A 2073 2.13 REMARK 500 O2 SO4 A 1509 O HOH A 1601 2.15 REMARK 500 O HOH A 1719 O HOH A 2083 2.15 REMARK 500 O HOH A 1846 O HOH A 1991 2.18 REMARK 500 O HOH A 2123 O HOH A 2210 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 1607 O HOH A 1764 4545 2.12 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 ASN A 993 72.09 -152.78 REMARK 500 ALA A1008 -119.52 48.47 REMARK 500 SER A1025 85.30 -158.54 REMARK 500 SER A1025 85.30 -159.53 REMARK 500 ARG A1048 38.47 -81.55 REMARK 500 GLU A1049 -9.62 65.55 REMARK 500 ILE A1333 -61.77 -92.07 REMARK 500 ASP A1340 -56.27 77.02 REMARK 500 SER A1366 87.64 -154.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2227 DISTANCE = 7.27 ANGSTROMS 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 A1502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1146 NE2 REMARK 620 2 GLU A1148 OE2 93.4 REMARK 620 3 HIS A1226 NE2 85.4 88.4 REMARK 620 4 E7Z A1501 O1 89.5 176.0 89.0 REMARK 620 5 E7Z A1501 O4 98.4 98.9 171.5 83.4 REMARK 620 6 HOH A1759 O 173.0 88.6 88.0 88.2 87.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1331 SG REMARK 620 2 CYS A1334 SG 110.9 REMARK 620 3 CYS A1358 SG 112.0 110.5 REMARK 620 4 CYS A1361 SG 108.2 111.9 103.2 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 E7Z A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 1509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG0 A 1510 DBREF 6FUL A 877 1401 UNP O15550 KDM6A_HUMAN 877 1401 SEQADV 6FUL GLY A 871 UNP O15550 EXPRESSION TAG SEQADV 6FUL PRO A 872 UNP O15550 EXPRESSION TAG SEQADV 6FUL GLY A 873 UNP O15550 EXPRESSION TAG SEQADV 6FUL TYR A 874 UNP O15550 EXPRESSION TAG SEQADV 6FUL GLN A 875 UNP O15550 EXPRESSION TAG SEQADV 6FUL ASP A 876 UNP O15550 EXPRESSION TAG SEQADV 6FUL ASN A 878 UNP O15550 SER 878 CONFLICT SEQADV 6FUL SER A 879 UNP O15550 PRO 879 CONFLICT SEQRES 1 A 531 GLY PRO GLY TYR GLN ASP PRO ASN SER GLN ILE ILE PRO SEQRES 2 A 531 SER MET SER VAL SER ILE TYR PRO SER SER ALA GLU VAL SEQRES 3 A 531 LEU LYS ALA CYS ARG ASN LEU GLY LYS ASN GLY LEU SER SEQRES 4 A 531 ASN SER SER ILE LEU LEU ASP LYS CYS PRO PRO PRO ARG SEQRES 5 A 531 PRO PRO SER SER PRO TYR PRO PRO LEU PRO LYS ASP LYS SEQRES 6 A 531 LEU ASN PRO PRO THR PRO SER ILE TYR LEU GLU ASN LYS SEQRES 7 A 531 ARG ASP ALA PHE PHE PRO PRO LEU HIS GLN PHE CYS THR SEQRES 8 A 531 ASN PRO ASN ASN PRO VAL THR VAL ILE ARG GLY LEU ALA SEQRES 9 A 531 GLY ALA LEU LYS LEU ASP LEU GLY LEU PHE SER THR LYS SEQRES 10 A 531 THR LEU VAL GLU ALA ASN ASN GLU HIS MET VAL GLU VAL SEQRES 11 A 531 ARG THR GLN LEU LEU GLN PRO ALA ASP GLU ASN TRP ASP SEQRES 12 A 531 PRO THR GLY THR LYS LYS ILE TRP HIS CYS GLU SER ASN SEQRES 13 A 531 ARG SER HIS THR THR ILE ALA LYS TYR ALA GLN TYR GLN SEQRES 14 A 531 ALA SER SER PHE GLN GLU SER LEU ARG GLU GLU ASN GLU SEQRES 15 A 531 LYS ARG SER HIS HIS LYS ASP HIS SER ASP SER GLU SER SEQRES 16 A 531 THR SER SER ASP ASN SER GLY ARG ARG ARG LYS GLY PRO SEQRES 17 A 531 PHE LYS THR ILE LYS PHE GLY THR ASN ILE ASP LEU SER SEQRES 18 A 531 ASP ASP LYS LYS TRP LYS LEU GLN LEU HIS GLU LEU THR SEQRES 19 A 531 LYS LEU PRO ALA PHE VAL ARG VAL VAL SER ALA GLY ASN SEQRES 20 A 531 LEU LEU SER HIS VAL GLY HIS THR ILE LEU GLY MET ASN SEQRES 21 A 531 THR VAL GLN LEU TYR MET LYS VAL PRO GLY SER ARG THR SEQRES 22 A 531 PRO GLY HIS GLN GLU ASN ASN ASN PHE CYS SER VAL ASN SEQRES 23 A 531 ILE ASN ILE GLY PRO GLY ASP CYS GLU TRP PHE VAL VAL SEQRES 24 A 531 PRO GLU GLY TYR TRP GLY VAL LEU ASN ASP PHE CYS GLU SEQRES 25 A 531 LYS ASN ASN LEU ASN PHE LEU MET GLY SER TRP TRP PRO SEQRES 26 A 531 ASN LEU GLU ASP LEU TYR GLU ALA ASN VAL PRO VAL TYR SEQRES 27 A 531 ARG PHE ILE GLN ARG PRO GLY ASP LEU VAL TRP ILE ASN SEQRES 28 A 531 ALA GLY THR VAL HIS TRP VAL GLN ALA ILE GLY TRP CYS SEQRES 29 A 531 ASN ASN ILE ALA TRP ASN VAL GLY PRO LEU THR ALA CYS SEQRES 30 A 531 GLN TYR LYS LEU ALA VAL GLU ARG TYR GLU TRP ASN LYS SEQRES 31 A 531 LEU GLN SER VAL LYS SER ILE VAL PRO MET VAL HIS LEU SEQRES 32 A 531 SER TRP ASN MET ALA ARG ASN ILE LYS VAL SER ASP PRO SEQRES 33 A 531 LYS LEU PHE GLU MET ILE LYS TYR CYS LEU LEU ARG THR SEQRES 34 A 531 LEU LYS GLN CYS GLN THR LEU ARG GLU ALA LEU ILE ALA SEQRES 35 A 531 ALA GLY LYS GLU ILE ILE TRP HIS GLY ARG THR LYS GLU SEQRES 36 A 531 GLU PRO ALA HIS TYR CYS SER ILE CYS GLU VAL GLU VAL SEQRES 37 A 531 PHE ASP LEU LEU PHE VAL THR ASN GLU SER ASN SER ARG SEQRES 38 A 531 LYS THR TYR ILE VAL HIS CYS GLN ASP CYS ALA ARG LYS SEQRES 39 A 531 THR SER GLY ASN LEU GLU ASN PHE VAL VAL LEU GLU GLN SEQRES 40 A 531 TYR LYS MET GLU ASP LEU MET GLN VAL TYR ASP GLN PHE SEQRES 41 A 531 THR LEU ALA PRO PRO LEU PRO SER ALA SER SER HET E7Z A1501 12 HET MN A1502 1 HET ZN A1503 1 HET SO4 A1504 5 HET SO4 A1505 5 HET SO4 A1506 5 HET SO4 A1507 5 HET SO4 A1508 5 HET SO4 A1509 5 HET PG0 A1510 8 HETNAM E7Z 1-METHYL-5-OXIDANYL-4-OXIDANYLIDENE-PYRIDINE-2- HETNAM 2 E7Z CARBOXYLIC ACID HETNAM MN MANGANESE (II) ION HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM PG0 2-(2-METHOXYETHOXY)ETHANOL HETSYN PG0 PEG 6000 FORMUL 2 E7Z C7 H7 N O4 FORMUL 3 MN MN 2+ FORMUL 4 ZN ZN 2+ FORMUL 5 SO4 6(O4 S 2-) FORMUL 11 PG0 C5 H12 O3 FORMUL 12 HOH *627(H2 O) HELIX 1 AA1 SER A 892 ARG A 901 1 10 HELIX 2 AA2 PRO A 932 LEU A 936 5 5 HELIX 3 AA3 ASN A 947 PHE A 952 1 6 HELIX 4 AA4 PRO A 954 ASN A 962 1 9 HELIX 5 AA5 GLY A 972 LYS A 978 1 7 HELIX 6 AA6 ASP A 980 PHE A 984 5 5 HELIX 7 AA7 SER A 985 ASN A 994 1 10 HELIX 8 AA8 ILE A 1032 ARG A 1048 1 17 HELIX 9 AA9 TRP A 1096 THR A 1104 1 9 HELIX 10 AB1 LYS A 1105 LEU A 1106 5 2 HELIX 11 AB2 PRO A 1107 ARG A 1111 5 5 HELIX 12 AB3 ASN A 1117 VAL A 1122 5 6 HELIX 13 AB4 GLU A 1148 PHE A 1152 5 5 HELIX 14 AB5 PRO A 1170 GLY A 1172 5 3 HELIX 15 AB6 TYR A 1173 ASN A 1184 1 12 HELIX 16 AB7 ASN A 1196 ALA A 1203 1 8 HELIX 17 AB8 THR A 1245 SER A 1263 1 19 HELIX 18 AB9 PRO A 1269 ILE A 1281 1 13 HELIX 19 AC1 ASP A 1285 ALA A 1313 1 29 HELIX 20 AC2 ASN A 1346 ARG A 1351 1 6 HELIX 21 AC3 CYS A 1358 SER A 1366 1 9 HELIX 22 AC4 LYS A 1379 PHE A 1390 1 12 SHEET 1 AA1 9 SER A 942 TYR A 944 0 SHEET 2 AA1 9 VAL A 967 ARG A 971 1 O ARG A 971 N ILE A 943 SHEET 3 AA1 9 LEU A1217 ILE A1220 -1 O LEU A1217 N ILE A 970 SHEET 4 AA1 9 CYS A1153 PRO A1161 -1 N ASN A1156 O VAL A1218 SHEET 5 AA1 9 CYS A1234 VAL A1241 -1 O ASN A1235 N ILE A1159 SHEET 6 AA1 9 GLN A1133 LYS A1137 -1 N TYR A1135 O ASN A1236 SHEET 7 AA1 9 THR A1081 ASP A1089 -1 N GLY A1085 O MET A1136 SHEET 8 AA1 9 MET A 997 LEU A1004 -1 N GLN A1003 O ILE A1082 SHEET 9 AA1 9 SER A1025 THR A1031 -1 O ASN A1026 N THR A1002 SHEET 1 AA2 4 ARG A1142 HIS A1146 0 SHEET 2 AA2 4 VAL A1225 ALA A1230 -1 O VAL A1228 N THR A1143 SHEET 3 AA2 4 CYS A1164 VAL A1169 -1 N VAL A1169 O VAL A1225 SHEET 4 AA2 4 TYR A1208 GLN A1212 -1 O GLN A1212 N CYS A1164 SHEET 1 AA3 3 ILE A1317 TRP A1319 0 SHEET 2 AA3 3 PHE A1372 GLU A1376 1 O VAL A1374 N ILE A1318 SHEET 3 AA3 3 LEU A1341 THR A1345 -1 N VAL A1344 O VAL A1373 SHEET 1 AA4 2 HIS A1329 TYR A1330 0 SHEET 2 AA4 2 GLU A1337 VAL A1338 -1 O VAL A1338 N HIS A1329 LINK N ALA A1115 O3 SO4 A1509 1555 1555 1.30 LINK NE2 HIS A1146 MN MN A1502 1555 1555 2.13 LINK OE2 GLU A1148 MN MN A1502 1555 1555 2.11 LINK NE2 HIS A1226 MN MN A1502 1555 1555 2.07 LINK SG CYS A1331 ZN ZN A1503 1555 1555 2.35 LINK SG CYS A1334 ZN ZN A1503 1555 1555 2.36 LINK SG CYS A1358 ZN ZN A1503 1555 1555 2.24 LINK SG CYS A1361 ZN ZN A1503 1555 1555 2.35 LINK O1 E7Z A1501 MN MN A1502 1555 1555 2.11 LINK O4 E7Z A1501 MN MN A1502 1555 1555 2.04 LINK MN MN A1502 O HOH A1759 1555 1555 2.07 CISPEP 1 TYR A 928 PRO A 929 0 -0.46 CISPEP 2 GLY A 1160 PRO A 1161 0 6.69 SITE 1 AC1 13 TYR A1135 LYS A1137 THR A1143 HIS A1146 SITE 2 AC1 13 GLU A1148 ASN A1156 HIS A1226 VAL A1228 SITE 3 AC1 13 MN A1502 HOH A1642 HOH A1759 HOH A1805 SITE 4 AC1 13 HOH A1842 SITE 1 AC2 5 HIS A1146 GLU A1148 HIS A1226 E7Z A1501 SITE 2 AC2 5 HOH A1759 SITE 1 AC3 4 CYS A1331 CYS A1334 CYS A1358 CYS A1361 SITE 1 AC4 5 LYS A 935 ARG A1027 HOH A1603 HOH A1607 SITE 2 AC4 5 HOH A1874 SITE 1 AC5 6 PHE A 952 PRO A1107 ALA A1108 ARG A1111 SITE 2 AC5 6 HOH A1650 HOH A1828 SITE 1 AC6 6 GLU A 946 LYS A1250 VAL A1253 MET A1291 SITE 2 AC6 6 HOH A1639 HOH A1961 SITE 1 AC7 6 ASN A 947 LYS A 948 ALA A 976 HOH A1605 SITE 2 AC7 6 HOH A1628 HOH A1632 SITE 1 AC8 9 ARG A1322 THR A1323 LYS A1324 GLU A1325 SITE 2 AC8 9 GLU A1326 HOH A1611 HOH A1676 HOH A1935 SITE 3 AC8 9 HOH A1978 SITE 1 AC9 6 ARG A1111 SER A1114 ALA A1115 GLY A1116 SITE 2 AC9 6 HOH A1601 HOH A1652 SITE 1 AD1 6 SER A1114 SER A1120 HIS A1121 ASN A1280 SITE 2 AD1 6 HOH A1601 HOH A1984 CRYST1 79.181 82.801 93.156 90.00 90.00 90.00 P 21 21 21 4 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 0.012629 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010735 0.00000