HEADER OXIDOREDUCTASE 07-SEP-17 5OY3 TITLE THE STRUCTURAL BASIS OF THE HISTONE DEMETHYLASE KDM6B HISTONE 3 LYSINE TITLE 2 27 SPECIFICITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 6B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING PROTEIN 3,JUMONJI DOMAIN-CONTAINING COMPND 5 PROTEIN 3,LYSINE DEMETHYLASE 6B; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: HISTONE 3 PEPTIDE H3(17-33)A21M; COMPND 10 CHAIN: B; COMPND 11 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: KDM6B, JMJD3, KIAA0346; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS EPIGENETICS, HISTONE DEMETHYLASE, SUBSTRATE COMPLEX, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.E.JONES,L.OLSEN,M.GAJHEDE REVDAT 3 17-JAN-24 5OY3 1 REMARK REVDAT 2 03-APR-19 5OY3 1 JRNL REVDAT 1 20-SEP-17 5OY3 0 JRNL AUTH S.E.JONES,L.OLSEN,M.GAJHEDE JRNL TITL STRUCTURAL BASIS OF HISTONE DEMETHYLASE KDM6B HISTONE 3 JRNL TITL 2 LYSINE 27 SPECIFICITY. JRNL REF BIOCHEMISTRY V. 57 585 2018 JRNL REFN ISSN 0006-2960 JRNL PMID 29220567 JRNL DOI 10.1021/ACS.BIOCHEM.7B01152 REMARK 2 REMARK 2 RESOLUTION. 2.14 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 2.14 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 31572 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.330 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 48.7383 - 5.1458 1.00 2334 158 0.1664 0.1886 REMARK 3 2 5.1458 - 4.0850 1.00 2182 147 0.1213 0.1651 REMARK 3 3 4.0850 - 3.5688 1.00 2149 146 0.1364 0.2060 REMARK 3 4 3.5688 - 3.2426 1.00 2131 144 0.1642 0.2192 REMARK 3 5 3.2426 - 3.0102 1.00 2100 142 0.1650 0.2598 REMARK 3 6 3.0102 - 2.8327 1.00 2109 143 0.1684 0.2194 REMARK 3 7 2.8327 - 2.6909 1.00 2098 142 0.1702 0.2383 REMARK 3 8 2.6909 - 2.5738 1.00 2079 140 0.1739 0.2541 REMARK 3 9 2.5738 - 2.4747 1.00 2087 141 0.1790 0.2467 REMARK 3 10 2.4747 - 2.3893 1.00 2065 140 0.1918 0.2450 REMARK 3 11 2.3893 - 2.3146 1.00 2086 140 0.1963 0.2742 REMARK 3 12 2.3146 - 2.2484 1.00 2072 141 0.2297 0.2907 REMARK 3 13 2.2484 - 2.1892 1.00 2068 140 0.2424 0.2949 REMARK 3 14 2.1892 - 2.1358 0.99 2012 136 0.2454 0.3085 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) : 21.730 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 : 0.012 3880 REMARK 3 ANGLE : 1.109 5259 REMARK 3 CHIRALITY : 0.064 571 REMARK 3 PLANARITY : 0.007 675 REMARK 3 DIHEDRAL : 14.809 2305 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 5OY3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1200004988. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31653 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.136 REMARK 200 RESOLUTION RANGE LOW (A) : 48.726 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.17400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.39700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHASER REMARK 200 STARTING MODEL: 3AVR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 7.5, 15%(V/V) TERT REMARK 280 -BUTANOL,, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 114.23800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.45400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.45400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.11900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.45400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.45400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 171.35700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.45400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.45400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.11900 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.45400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.45400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 171.35700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 114.23800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 ASP A 1141 REMARK 465 VAL A 1142 REMARK 465 VAL A 1143 REMARK 465 ARG A 1144 REMARK 465 ALA A 1145 REMARK 465 SER A 1146 REMARK 465 ARG A 1147 REMARK 465 ASN A 1148 REMARK 465 ALA A 1149 REMARK 465 LYS A 1150 REMARK 465 VAL A 1151 REMARK 465 LYS A 1152 REMARK 465 GLY A 1153 REMARK 465 LYS A 1154 REMARK 465 PHE A 1155 REMARK 465 ARG A 1156 REMARK 465 LEU A 1292 REMARK 465 GLN A 1293 REMARK 465 GLU A 1294 REMARK 465 GLU A 1295 REMARK 465 LYS A 1296 REMARK 465 GLU A 1297 REMARK 465 SER A 1298 REMARK 465 GLU A 1299 REMARK 465 ASP A 1300 REMARK 465 GLU A 1301 REMARK 465 GLU A 1302 REMARK 465 SER A 1303 REMARK 465 GLU A 1304 REMARK 465 GLU A 1305 REMARK 465 PRO A 1306 REMARK 465 ASP A 1307 REMARK 465 SER A 1308 REMARK 465 THR A 1309 REMARK 465 THR A 1310 REMARK 465 GLY A 1311 REMARK 465 THR A 1312 REMARK 465 PRO A 1313 REMARK 465 PRO A 1314 REMARK 465 SER A 1315 REMARK 465 SER A 1316 REMARK 465 ALA A 1317 REMARK 465 PRO A 1318 REMARK 465 ASP A 1319 REMARK 465 PRO A 1320 REMARK 465 LYS A 1321 REMARK 465 ASN A 1322 REMARK 465 HIS A 1323 REMARK 465 ASN A 1592 REMARK 465 SER A 1640 REMARK 465 THR A 1641 REMARK 465 SER A 1642 REMARK 465 ARG A 1643 REMARK 465 HIS A 1644 REMARK 465 HIS A 1645 REMARK 465 HIS A 1646 REMARK 465 HIS A 1647 REMARK 465 HIS A 1648 REMARK 465 HIS A 1649 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 OE1 GLU A 1409 HH21 ARG A 1453 1.53 REMARK 500 O SER A 1610 H LEU A 1613 1.55 REMARK 500 O HOH B 110 O HOH B 120 1.88 REMARK 500 O HOH A 2006 O HOH B 119 2.02 REMARK 500 O HOH A 1908 O HOH A 2054 2.07 REMARK 500 O HOH A 1838 O HOH A 1965 2.11 REMARK 500 O ARG A 1216 O HOH A 1801 2.12 REMARK 500 O HOH A 1951 O HOH B 116 2.17 REMARK 500 O GLY A 1593 O HOH A 1802 2.19 REMARK 500 O HOH A 2017 O HOH A 2042 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 THR A1172 -31.53 67.93 REMARK 500 SER A1270 92.71 -161.52 REMARK 500 LEU A1334 53.31 -104.60 REMARK 500 MET A1373 -60.98 -109.70 REMARK 500 ASN A1584 -69.77 77.26 REMARK 500 SER A1610 86.78 -165.93 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 FE A1701 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A1390 NE2 REMARK 620 2 GLU A1392 OE2 92.3 REMARK 620 3 HIS A1470 NE2 87.1 87.3 REMARK 620 4 AKG A1703 O2 166.9 99.5 98.8 REMARK 620 5 AKG A1703 O5 90.9 171.8 100.3 76.6 REMARK 620 6 HOH A1956 O 89.2 81.9 168.5 87.2 90.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1702 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1575 SG REMARK 620 2 CYS A1578 SG 111.6 REMARK 620 3 CYS A1602 SG 114.4 112.2 REMARK 620 4 CYS A1605 SG 106.2 110.5 101.2 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 FE A 1701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 1703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1706 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1707 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1708 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1709 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1710 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1711 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TBU A 1712 DBREF 5OY3 A 1141 1643 UNP O15054 KDM6B_HUMAN 1141 1643 DBREF 5OY3 B 17 33 PDB 5OY3 5OY3 17 33 SEQADV 5OY3 HIS A 1644 UNP O15054 EXPRESSION TAG SEQADV 5OY3 HIS A 1645 UNP O15054 EXPRESSION TAG SEQADV 5OY3 HIS A 1646 UNP O15054 EXPRESSION TAG SEQADV 5OY3 HIS A 1647 UNP O15054 EXPRESSION TAG SEQADV 5OY3 HIS A 1648 UNP O15054 EXPRESSION TAG SEQADV 5OY3 HIS A 1649 UNP O15054 EXPRESSION TAG SEQRES 1 A 509 ASP VAL VAL ARG ALA SER ARG ASN ALA LYS VAL LYS GLY SEQRES 2 A 509 LYS PHE ARG GLU SER TYR LEU SER PRO ALA GLN SER VAL SEQRES 3 A 509 LYS PRO LYS ILE ASN THR GLU GLU LYS LEU PRO ARG GLU SEQRES 4 A 509 LYS LEU ASN PRO PRO THR PRO SER ILE TYR LEU GLU SER SEQRES 5 A 509 LYS ARG ASP ALA PHE SER PRO VAL LEU LEU GLN PHE CYS SEQRES 6 A 509 THR ASP PRO ARG ASN PRO ILE THR VAL ILE ARG GLY LEU SEQRES 7 A 509 ALA GLY SER LEU ARG LEU ASN LEU GLY LEU PHE SER THR SEQRES 8 A 509 LYS THR LEU VAL GLU ALA SER GLY GLU HIS THR VAL GLU SEQRES 9 A 509 VAL ARG THR GLN VAL GLN GLN PRO SER ASP GLU ASN TRP SEQRES 10 A 509 ASP LEU THR GLY THR ARG GLN ILE TRP PRO CYS GLU SER SEQRES 11 A 509 SER ARG SER HIS THR THR ILE ALA LYS TYR ALA GLN TYR SEQRES 12 A 509 GLN ALA SER SER PHE GLN GLU SER LEU GLN GLU GLU LYS SEQRES 13 A 509 GLU SER GLU ASP GLU GLU SER GLU GLU PRO ASP SER THR SEQRES 14 A 509 THR GLY THR PRO PRO SER SER ALA PRO ASP PRO LYS ASN SEQRES 15 A 509 HIS HIS ILE ILE LYS PHE GLY THR ASN ILE ASP LEU SER SEQRES 16 A 509 ASP ALA LYS ARG TRP LYS PRO GLN LEU GLN GLU LEU LEU SEQRES 17 A 509 LYS LEU PRO ALA PHE MET ARG VAL THR SER THR GLY ASN SEQRES 18 A 509 MET LEU SER HIS VAL GLY HIS THR ILE LEU GLY MET ASN SEQRES 19 A 509 THR VAL GLN LEU TYR MET LYS VAL PRO GLY SER ARG THR SEQRES 20 A 509 PRO GLY HIS GLN GLU ASN ASN ASN PHE CYS SER VAL ASN SEQRES 21 A 509 ILE ASN ILE GLY PRO GLY ASP CYS GLU TRP PHE ALA VAL SEQRES 22 A 509 HIS GLU HIS TYR TRP GLU THR ILE SER ALA PHE CYS ASP SEQRES 23 A 509 ARG HIS GLY VAL ASP TYR LEU THR GLY SER TRP TRP PRO SEQRES 24 A 509 ILE LEU ASP ASP LEU TYR ALA SER ASN ILE PRO VAL TYR SEQRES 25 A 509 ARG PHE VAL GLN ARG PRO GLY ASP LEU VAL TRP ILE ASN SEQRES 26 A 509 ALA GLY THR VAL HIS TRP VAL GLN ALA THR GLY TRP CYS SEQRES 27 A 509 ASN ASN ILE ALA TRP ASN VAL GLY PRO LEU THR ALA TYR SEQRES 28 A 509 GLN TYR GLN LEU ALA LEU GLU ARG TYR GLU TRP ASN GLU SEQRES 29 A 509 VAL LYS ASN VAL LYS SER ILE VAL PRO MET ILE HIS VAL SEQRES 30 A 509 SER TRP ASN VAL ALA ARG THR VAL LYS ILE SER ASP PRO SEQRES 31 A 509 ASP LEU PHE LYS MET ILE LYS PHE CYS LEU LEU GLN SER SEQRES 32 A 509 MET LYS HIS CYS GLN VAL GLN ARG GLU SER LEU VAL ARG SEQRES 33 A 509 ALA GLY LYS LYS ILE ALA TYR GLN GLY ARG VAL LYS ASP SEQRES 34 A 509 GLU PRO ALA TYR TYR CYS ASN GLU CYS ASP VAL GLU VAL SEQRES 35 A 509 PHE ASN ILE LEU PHE VAL THR SER GLU ASN GLY SER ARG SEQRES 36 A 509 ASN THR TYR LEU VAL HIS CYS GLU GLY CYS ALA ARG ARG SEQRES 37 A 509 ARG SER ALA GLY LEU GLN GLY VAL VAL VAL LEU GLU GLN SEQRES 38 A 509 TYR ARG THR GLU GLU LEU ALA GLN ALA TYR ASP ALA PHE SEQRES 39 A 509 THR LEU ALA PRO ALA SER THR SER ARG HIS HIS HIS HIS SEQRES 40 A 509 HIS HIS SEQRES 1 B 17 ARG LYS GLN LEU MET THR LYS ALA ALA ARG LYS SER ALA SEQRES 2 B 17 PRO ALA THR GLY HET FE A1701 1 HET ZN A1702 1 HET AKG A1703 14 HET EDO A1704 10 HET EDO A1705 10 HET EDO A1706 10 HET EDO A1707 10 HET EDO A1708 10 HET EDO A1709 10 HET EDO A1710 10 HET EDO A1711 10 HET TBU A1712 15 HETNAM FE FE (III) ION HETNAM ZN ZINC ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM TBU TERTIARY-BUTYL ALCOHOL HETSYN EDO ETHYLENE GLYCOL HETSYN TBU 2-METHYL-2-PROPANOL FORMUL 3 FE FE 3+ FORMUL 4 ZN ZN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 EDO 8(C2 H6 O2) FORMUL 14 TBU C4 H10 O FORMUL 15 HOH *300(H2 O) HELIX 1 AA1 SER A 1161 SER A 1165 5 5 HELIX 2 AA2 PRO A 1177 ASN A 1182 1 6 HELIX 3 AA3 SER A 1192 PHE A 1197 1 6 HELIX 4 AA4 SER A 1198 ASP A 1207 1 10 HELIX 5 AA5 GLY A 1217 ARG A 1223 1 7 HELIX 6 AA6 ASN A 1225 PHE A 1229 5 5 HELIX 7 AA7 SER A 1230 SER A 1238 1 9 HELIX 8 AA8 ILE A 1277 GLN A 1289 1 13 HELIX 9 AA9 TRP A 1340 LEU A 1347 1 8 HELIX 10 AB1 LEU A 1348 LEU A 1350 5 3 HELIX 11 AB2 PRO A 1351 ARG A 1355 5 5 HELIX 12 AB3 ASN A 1361 VAL A 1366 5 6 HELIX 13 AB4 GLU A 1392 PHE A 1396 5 5 HELIX 14 AB5 HIS A 1414 HIS A 1416 5 3 HELIX 15 AB6 TYR A 1417 HIS A 1428 1 12 HELIX 16 AB7 ILE A 1440 SER A 1447 1 8 HELIX 17 AB8 THR A 1489 ASN A 1507 1 19 HELIX 18 AB9 PRO A 1513 VAL A 1525 1 13 HELIX 19 AC1 ASP A 1529 ALA A 1557 1 29 HELIX 20 AC2 CYS A 1602 SER A 1610 1 9 HELIX 21 AC3 ARG A 1623 PHE A 1634 1 12 SHEET 1 AA1 9 SER A1187 TYR A1189 0 SHEET 2 AA1 9 ILE A1212 ARG A1216 1 O ARG A1216 N ILE A1188 SHEET 3 AA1 9 LEU A1461 ILE A1464 -1 O TRP A1463 N THR A1213 SHEET 4 AA1 9 CYS A1397 ASN A1402 -1 N SER A1398 O ILE A1464 SHEET 5 AA1 9 CYS A1478 VAL A1485 -1 O ILE A1481 N ILE A1401 SHEET 6 AA1 9 GLN A1377 LYS A1381 -1 N TYR A1379 O ASN A1480 SHEET 7 AA1 9 ILE A1325 ASP A1333 -1 N ILE A1332 O LEU A1378 SHEET 8 AA1 9 THR A1242 VAL A1249 -1 N GLN A1248 O ILE A1326 SHEET 9 AA1 9 SER A1271 THR A1276 -1 O THR A1275 N VAL A1243 SHEET 1 AA2 2 ILE A1370 LEU A1371 0 SHEET 2 AA2 2 ALA B 25 ARG B 26 1 O ALA B 25 N LEU A1371 SHEET 1 AA3 4 ARG A1386 HIS A1390 0 SHEET 2 AA3 4 VAL A1469 ALA A1474 -1 O VAL A1472 N THR A1387 SHEET 3 AA3 4 CYS A1408 VAL A1413 -1 N GLU A1409 O GLN A1473 SHEET 4 AA3 4 TYR A1452 GLN A1456 -1 O GLN A1456 N CYS A1408 SHEET 1 AA4 5 ALA A1562 TYR A1563 0 SHEET 2 AA4 5 VAL A1617 GLU A1620 1 O VAL A1618 N ALA A1562 SHEET 3 AA4 5 ILE A1585 THR A1589 -1 N VAL A1588 O VAL A1617 SHEET 4 AA4 5 THR A1597 HIS A1601 -1 O LEU A1599 N THR A1589 SHEET 5 AA4 5 GLN B 19 LEU B 20 1 O GLN B 19 N TYR A1598 LINK NE2 HIS A1390 FE FE A1701 1555 1555 2.17 LINK OE2 GLU A1392 FE FE A1701 1555 1555 2.08 LINK NE2 HIS A1470 FE FE A1701 1555 1555 2.14 LINK SG CYS A1575 ZN ZN A1702 1555 1555 2.27 LINK SG CYS A1578 ZN ZN A1702 1555 1555 2.32 LINK SG CYS A1602 ZN ZN A1702 1555 1555 2.48 LINK SG CYS A1605 ZN ZN A1702 1555 1555 2.37 LINK FE FE A1701 O2 AKG A1703 1555 1555 2.18 LINK FE FE A1701 O5 AKG A1703 1555 1555 2.36 LINK FE FE A1701 O HOH A1956 1555 1555 2.59 SITE 1 AC1 5 HIS A1390 GLU A1392 HIS A1470 AKG A1703 SITE 2 AC1 5 HOH A1956 SITE 1 AC2 4 CYS A1575 CYS A1578 CYS A1602 CYS A1605 SITE 1 AC3 11 LYS A1381 THR A1387 HIS A1390 GLU A1392 SITE 2 AC3 11 SER A1398 ASN A1400 HIS A1470 ASN A1480 SITE 3 AC3 11 ALA A1482 FE A1701 HOH A1942 SITE 1 AC4 7 LEU A1202 PHE A1353 GLY A1360 PRO A1487 SITE 2 AC4 7 LEU A1488 HOH A1804 HOH A1900 SITE 1 AC5 4 SER A1187 ILE A1188 HOH A1858 HOH A1963 SITE 1 AC6 6 LYS A1167 GLU A1415 HIS A1416 TRP A1418 SITE 2 AC6 6 GLU A1419 HOH A1806 SITE 1 AC7 8 LEU A1181 ASN A1182 LEU A1441 TYR A1445 SITE 2 AC7 8 ILE A1449 VAL A1451 HOH A1809 HOH A1935 SITE 1 AC8 9 GLN A1250 GLN A1251 PRO A1252 GLY A1384 SITE 2 AC8 9 GLN A1473 ARG A1556 ALA A1557 GLY A1558 SITE 3 AC8 9 HOH A1943 SITE 1 AC9 5 TRP A1519 ASN A1520 ARG A1523 TYR A1622 SITE 2 AC9 5 HOH A1839 SITE 1 AD1 5 GLN A1284 ALA A1285 PHE A1288 TRP A1477 SITE 2 AD1 5 HOH A1959 SITE 1 AD2 7 THR A1242 GLU A1419 SER A1422 ALA A1423 SITE 2 AD2 7 ASP A1426 TBU A1712 HOH A1811 SITE 1 AD3 5 THR A1242 GLU A1244 EDO A1711 HOH A2051 SITE 2 AD3 5 ARG B 26 CRYST1 68.908 68.908 228.476 90.00 90.00 90.00 P 41 21 2 8 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 0.014512 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014512 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004377 0.00000