HEADER OXIDOREDUCTASE 05-DEC-17 6F6D TITLE THE CATALYTIC DOMAIN OF KDM6B IN COMPLEX WITH H3(17-33)K18IA21M TITLE 2 PEPTIDE 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)K18IA21M; 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_TAXID: 7108; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS EPIGENETICS, HISTONE DEMETHYLASE, SUBSTRATE BASED INHIBITOR, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.E.JONES,L.OLSEN,M.GAJHEDE REVDAT 2 17-JAN-24 6F6D 1 REMARK REVDAT 1 17-OCT-18 6F6D 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 1520-4995 JRNL PMID 29220567 JRNL DOI 10.1021/ACS.BIOCHEM.7B01152 REMARK 2 REMARK 2 RESOLUTION. 1.82 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 48866 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.982 REMARK 3 FREE R VALUE TEST SET COUNT : 1946 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 57.5287 - 4.3813 1.00 3768 157 0.1573 0.1939 REMARK 3 2 4.3813 - 3.4777 1.00 3544 148 0.1449 0.1932 REMARK 3 3 3.4777 - 3.0381 1.00 3506 145 0.1626 0.2024 REMARK 3 4 3.0381 - 2.7603 1.00 3471 146 0.1672 0.2052 REMARK 3 5 2.7603 - 2.5625 1.00 3454 144 0.1607 0.1878 REMARK 3 6 2.5625 - 2.4114 1.00 3423 142 0.1601 0.2356 REMARK 3 7 2.4114 - 2.2906 1.00 3406 143 0.1518 0.2234 REMARK 3 8 2.2906 - 2.1909 0.99 3392 141 0.1606 0.2054 REMARK 3 9 2.1909 - 2.1066 0.99 3365 138 0.1751 0.2224 REMARK 3 10 2.1066 - 2.0339 0.97 3321 141 0.1809 0.2440 REMARK 3 11 2.0339 - 1.9703 0.97 3285 136 0.1920 0.2794 REMARK 3 12 1.9703 - 1.9140 0.95 3220 132 0.2197 0.3066 REMARK 3 13 1.9140 - 1.8636 0.79 2655 106 0.2680 0.3421 REMARK 3 14 1.8636 - 1.8181 0.91 3110 127 0.2402 0.3476 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) : 0.209 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.26 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 : 0.010 3880 REMARK 3 ANGLE : 1.033 5285 REMARK 3 CHIRALITY : 0.059 577 REMARK 3 PLANARITY : 0.007 680 REMARK 3 DIHEDRAL : 15.737 2329 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 6F6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007419. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.1.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49999 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.818 REMARK 200 RESOLUTION RANGE LOW (A) : 65.633 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5OY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH 8.0, 15%(V/V) TERT REMARK 280 -BUTANOL,, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.0K 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 115.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 34.24000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.24000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.50000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.24000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 34.24000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 172.50000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 34.24000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.24000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.50000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 34.24000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.24000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 172.50000 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 115.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 MET A 1140 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 ALA A 1639 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 O HOH A 2197 O HOH A 2203 2.00 REMARK 500 O ARG A 1216 O HOH A 1801 2.06 REMARK 500 O HOH A 1959 O HOH A 2001 2.09 REMARK 500 O HOH A 2063 O HOH A 2123 2.13 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 1812 O HOH A 1979 7635 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A1386 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES 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 SER A1270 90.68 -162.57 REMARK 500 THR A1275 -159.52 -160.09 REMARK 500 LEU A1334 50.80 -106.87 REMARK 500 MET A1373 -62.20 -105.18 REMARK 500 ASN A1448 30.49 72.32 REMARK 500 ASN A1584 -66.14 75.06 REMARK 500 ARG A1609 -72.16 -68.63 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 91.6 REMARK 620 3 HIS A1470 NE2 87.5 86.8 REMARK 620 4 AKG A1703 O2 169.4 97.6 98.1 REMARK 620 5 AKG A1703 O5 91.1 175.8 96.5 79.4 REMARK 620 6 HOH A2098 O 88.3 88.7 173.8 86.7 88.2 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 108.7 REMARK 620 3 CYS A1602 SG 114.6 113.7 REMARK 620 4 CYS A1605 SG 104.6 113.8 101.1 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 TBU A 1704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TBU A 1705 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TBU A 1706 DBREF 6F6D A 1141 1643 UNP O15054 KDM6B_HUMAN 1141 1643 DBREF 6F6D B 17 33 PDB 6F6D 6F6D 17 33 SEQADV 6F6D MET A 1140 UNP O15054 INITIATING METHIONINE SEQADV 6F6D HIS A 1644 UNP O15054 EXPRESSION TAG SEQADV 6F6D HIS A 1645 UNP O15054 EXPRESSION TAG SEQADV 6F6D HIS A 1646 UNP O15054 EXPRESSION TAG SEQADV 6F6D HIS A 1647 UNP O15054 EXPRESSION TAG SEQADV 6F6D HIS A 1648 UNP O15054 EXPRESSION TAG SEQADV 6F6D HIS A 1649 UNP O15054 EXPRESSION TAG SEQRES 1 A 510 MET ASP VAL VAL ARG ALA SER ARG ASN ALA LYS VAL LYS SEQRES 2 A 510 GLY LYS PHE ARG GLU SER TYR LEU SER PRO ALA GLN SER SEQRES 3 A 510 VAL LYS PRO LYS ILE ASN THR GLU GLU LYS LEU PRO ARG SEQRES 4 A 510 GLU LYS LEU ASN PRO PRO THR PRO SER ILE TYR LEU GLU SEQRES 5 A 510 SER LYS ARG ASP ALA PHE SER PRO VAL LEU LEU GLN PHE SEQRES 6 A 510 CYS THR ASP PRO ARG ASN PRO ILE THR VAL ILE ARG GLY SEQRES 7 A 510 LEU ALA GLY SER LEU ARG LEU ASN LEU GLY LEU PHE SER SEQRES 8 A 510 THR LYS THR LEU VAL GLU ALA SER GLY GLU HIS THR VAL SEQRES 9 A 510 GLU VAL ARG THR GLN VAL GLN GLN PRO SER ASP GLU ASN SEQRES 10 A 510 TRP ASP LEU THR GLY THR ARG GLN ILE TRP PRO CYS GLU SEQRES 11 A 510 SER SER ARG SER HIS THR THR ILE ALA LYS TYR ALA GLN SEQRES 12 A 510 TYR GLN ALA SER SER PHE GLN GLU SER LEU GLN GLU GLU SEQRES 13 A 510 LYS GLU SER GLU ASP GLU GLU SER GLU GLU PRO ASP SER SEQRES 14 A 510 THR THR GLY THR PRO PRO SER SER ALA PRO ASP PRO LYS SEQRES 15 A 510 ASN HIS HIS ILE ILE LYS PHE GLY THR ASN ILE ASP LEU SEQRES 16 A 510 SER ASP ALA LYS ARG TRP LYS PRO GLN LEU GLN GLU LEU SEQRES 17 A 510 LEU LYS LEU PRO ALA PHE MET ARG VAL THR SER THR GLY SEQRES 18 A 510 ASN MET LEU SER HIS VAL GLY HIS THR ILE LEU GLY MET SEQRES 19 A 510 ASN THR VAL GLN LEU TYR MET LYS VAL PRO GLY SER ARG SEQRES 20 A 510 THR PRO GLY HIS GLN GLU ASN ASN ASN PHE CYS SER VAL SEQRES 21 A 510 ASN ILE ASN ILE GLY PRO GLY ASP CYS GLU TRP PHE ALA SEQRES 22 A 510 VAL HIS GLU HIS TYR TRP GLU THR ILE SER ALA PHE CYS SEQRES 23 A 510 ASP ARG HIS GLY VAL ASP TYR LEU THR GLY SER TRP TRP SEQRES 24 A 510 PRO ILE LEU ASP ASP LEU TYR ALA SER ASN ILE PRO VAL SEQRES 25 A 510 TYR ARG PHE VAL GLN ARG PRO GLY ASP LEU VAL TRP ILE SEQRES 26 A 510 ASN ALA GLY THR VAL HIS TRP VAL GLN ALA THR GLY TRP SEQRES 27 A 510 CYS ASN ASN ILE ALA TRP ASN VAL GLY PRO LEU THR ALA SEQRES 28 A 510 TYR GLN TYR GLN LEU ALA LEU GLU ARG TYR GLU TRP ASN SEQRES 29 A 510 GLU VAL LYS ASN VAL LYS SER ILE VAL PRO MET ILE HIS SEQRES 30 A 510 VAL SER TRP ASN VAL ALA ARG THR VAL LYS ILE SER ASP SEQRES 31 A 510 PRO ASP LEU PHE LYS MET ILE LYS PHE CYS LEU LEU GLN SEQRES 32 A 510 SER MET LYS HIS CYS GLN VAL GLN ARG GLU SER LEU VAL SEQRES 33 A 510 ARG ALA GLY LYS LYS ILE ALA TYR GLN GLY ARG VAL LYS SEQRES 34 A 510 ASP GLU PRO ALA TYR TYR CYS ASN GLU CYS ASP VAL GLU SEQRES 35 A 510 VAL PHE ASN ILE LEU PHE VAL THR SER GLU ASN GLY SER SEQRES 36 A 510 ARG ASN THR TYR LEU VAL HIS CYS GLU GLY CYS ALA ARG SEQRES 37 A 510 ARG ARG SER ALA GLY LEU GLN GLY VAL VAL VAL LEU GLU SEQRES 38 A 510 GLN TYR ARG THR GLU GLU LEU ALA GLN ALA TYR ASP ALA SEQRES 39 A 510 PHE THR LEU ALA PRO ALA SER THR SER ARG HIS HIS HIS SEQRES 40 A 510 HIS HIS HIS SEQRES 1 B 17 ARG ILE 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 TBU A1704 15 HET TBU A1705 15 HET TBU A1706 15 HETNAM FE FE (III) ION HETNAM ZN ZINC ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM TBU TERTIARY-BUTYL ALCOHOL HETSYN TBU 2-METHYL-2-PROPANOL FORMUL 3 FE FE 3+ FORMUL 4 ZN ZN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 TBU 3(C4 H10 O) FORMUL 9 HOH *453(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 LEU A 1222 1 6 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 GLU A 1290 1 14 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 PRO A1405 -1 N SER A1398 O ILE A1464 SHEET 5 AA1 9 CYS A1478 VAL A1485 -1 O ASN A1479 N ILE A1403 SHEET 6 AA1 9 GLN A1377 LYS A1381 -1 N LYS A1381 O CYS A1478 SHEET 7 AA1 9 ILE A1325 ASP A1333 -1 N GLY A1329 O MET A1380 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 SER A1273 N VAL A1245 SHEET 1 AA2 4 ARG A1386 HIS A1390 0 SHEET 2 AA2 4 VAL A1469 ALA A1474 -1 O HIS A1470 N HIS A1390 SHEET 3 AA2 4 CYS A1408 VAL A1413 -1 N GLU A1409 O GLN A1473 SHEET 4 AA2 4 TYR A1452 GLN A1456 -1 O GLN A1456 N CYS A1408 SHEET 1 AA3 5 ALA A1562 TYR A1563 0 SHEET 2 AA3 5 VAL A1617 GLU A1620 1 O VAL A1618 N ALA A1562 SHEET 3 AA3 5 ILE A1585 THR A1589 -1 N VAL A1588 O VAL A1617 SHEET 4 AA3 5 THR A1597 HIS A1601 -1 O LEU A1599 N THR A1589 SHEET 5 AA3 5 GLN B 19 LEU B 20 1 O GLN B 19 N TYR A1598 SHEET 1 AA4 2 TYR A1573 TYR A1574 0 SHEET 2 AA4 2 GLU A1581 VAL A1582 -1 O VAL A1582 N TYR A1573 LINK NE2 HIS A1390 FE FE A1701 1555 1555 2.17 LINK OE2 GLU A1392 FE FE A1701 1555 1555 2.01 LINK NE2 HIS A1470 FE FE A1701 1555 1555 2.12 LINK SG CYS A1575 ZN ZN A1702 1555 1555 2.35 LINK SG CYS A1578 ZN ZN A1702 1555 1555 2.35 LINK SG CYS A1602 ZN ZN A1702 1555 1555 2.31 LINK SG CYS A1605 ZN ZN A1702 1555 1555 2.28 LINK FE FE A1701 O2 AKG A1703 1555 1555 2.14 LINK FE FE A1701 O5 AKG A1703 1555 1555 2.23 LINK FE FE A1701 O HOH A2098 1555 1555 2.28 CISPEP 1 GLY A 1404 PRO A 1405 0 12.85 SITE 1 AC1 5 HIS A1390 GLU A1392 HIS A1470 AKG A1703 SITE 2 AC1 5 HOH A2098 SITE 1 AC2 4 CYS A1575 CYS A1578 CYS A1602 CYS A1605 SITE 1 AC3 13 LYS A1381 THR A1387 HIS A1390 GLU A1392 SITE 2 AC3 13 SER A1398 ASN A1400 HIS A1470 VAL A1472 SITE 3 AC3 13 ALA A1482 FE A1701 HOH A1815 HOH A1892 SITE 4 AC3 13 HOH A2098 SITE 1 AC4 3 HOH A1804 HOH A1813 HOH A1985 SITE 1 AC5 1 PHE A1288 SITE 1 AC6 4 THR A1242 HOH A2151 HOH A2168 ARG B 26 CRYST1 68.480 68.480 230.000 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 0.014603 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004348 0.00000