HEADER OXIDOREDUCTASE 07-MAR-11 3AVS TITLE CATALYTIC FRAGMENT OF UTX/KDM6A BOUND WITH N-OXYALYLGLYCINE, AND TITLE 2 NI(II) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 6A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 880-1401; COMPND 5 SYNONYM: HISTONE DEMETHYLASE UTX, UBIQUITOUSLY-TRANSCRIBED TPR COMPND 6 PROTEIN ON THE X CHROMOSOME, UBIQUITOUSLY-TRANSCRIBED X CHROMOSOME COMPND 7 TETRATRICOPEPTIDE REPEAT PROTEIN; 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 GENE: KDM6A, UTX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET47 KEYWDS CUPIN SUPERFAMILY, TRI/DIMETHYLLYSINE DEMETHYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.SENGOKU,S.YOKOYAMA REVDAT 3 13-MAR-24 3AVS 1 REMARK SEQADV LINK REVDAT 2 14-DEC-11 3AVS 1 JRNL REVDAT 1 19-OCT-11 3AVS 0 JRNL AUTH T.SENGOKU,S.YOKOYAMA JRNL TITL STRUCTURAL BASIS FOR HISTONE H3 LYS 27 DEMETHYLATION BY JRNL TITL 2 UTX/KDM6A JRNL REF GENES DEV. V. 25 2266 2011 JRNL REFN ISSN 0890-9369 JRNL PMID 22002947 JRNL DOI 10.1101/GAD.172296.111 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 50150 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2578 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 30.0698 - 4.8424 0.96 2875 139 0.1789 0.1817 REMARK 3 2 4.8424 - 3.8461 0.99 2827 155 0.1409 0.1707 REMARK 3 3 3.8461 - 3.3606 0.99 2773 165 0.1764 0.2164 REMARK 3 4 3.3606 - 3.0537 0.99 2783 142 0.1900 0.2301 REMARK 3 5 3.0537 - 2.8350 1.00 2766 138 0.1832 0.2250 REMARK 3 6 2.8350 - 2.6680 1.00 2764 161 0.1761 0.2123 REMARK 3 7 2.6680 - 2.5344 1.00 2768 148 0.1816 0.2417 REMARK 3 8 2.5344 - 2.4241 1.00 2762 153 0.1933 0.2180 REMARK 3 9 2.4241 - 2.3309 1.00 2757 141 0.1889 0.2472 REMARK 3 10 2.3309 - 2.2505 1.00 2750 147 0.1898 0.2186 REMARK 3 11 2.2505 - 2.1801 1.00 2729 146 0.1977 0.2481 REMARK 3 12 2.1801 - 2.1178 1.00 2755 154 0.2011 0.2642 REMARK 3 13 2.1178 - 2.0621 0.99 2711 148 0.2095 0.2584 REMARK 3 14 2.0621 - 2.0118 0.94 2575 120 0.2203 0.2719 REMARK 3 15 2.0118 - 1.9660 0.90 2447 139 0.2297 0.2756 REMARK 3 16 1.9660 - 1.9242 0.84 2321 130 0.2512 0.2767 REMARK 3 17 1.9242 - 1.8857 0.80 2176 125 0.2601 0.3139 REMARK 3 18 1.8857 - 1.8501 0.75 2033 127 0.2683 0.3054 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.89 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 36.67 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.230 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) : 4.50610 REMARK 3 B22 (A**2) : -1.98590 REMARK 3 B33 (A**2) : -2.52020 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 : 0.003 4003 REMARK 3 ANGLE : 0.811 5438 REMARK 3 CHIRALITY : 0.050 588 REMARK 3 PLANARITY : 0.003 702 REMARK 3 DIHEDRAL : 14.554 1485 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 886:927) REMARK 3 ORIGIN FOR THE GROUP (A): 41.4617 -26.0816 14.0518 REMARK 3 T TENSOR REMARK 3 T11: 0.7187 T22: 0.2973 REMARK 3 T33: 0.2596 T12: 0.1072 REMARK 3 T13: -0.0492 T23: 0.0183 REMARK 3 L TENSOR REMARK 3 L11: 0.3761 L22: 0.1384 REMARK 3 L33: 0.0718 L12: 0.0765 REMARK 3 L13: -0.0132 L23: -0.0959 REMARK 3 S TENSOR REMARK 3 S11: 0.2507 S12: -0.0086 S13: -0.0557 REMARK 3 S21: 0.1703 S22: -0.1058 S23: -0.0344 REMARK 3 S31: 0.0126 S32: -0.0047 S33: -0.0434 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 928:1261) REMARK 3 ORIGIN FOR THE GROUP (A): 24.3796 6.7336 14.5248 REMARK 3 T TENSOR REMARK 3 T11: 0.1617 T22: 0.1969 REMARK 3 T33: 0.1843 T12: 0.0012 REMARK 3 T13: -0.0073 T23: -0.0073 REMARK 3 L TENSOR REMARK 3 L11: 0.2493 L22: 1.1060 REMARK 3 L33: 1.3276 L12: 0.0310 REMARK 3 L13: 0.0869 L23: 0.2929 REMARK 3 S TENSOR REMARK 3 S11: -0.0395 S12: -0.0011 S13: -0.0247 REMARK 3 S21: -0.0018 S22: -0.0865 S23: -0.0389 REMARK 3 S31: -0.0843 S32: -0.1272 S33: 0.0598 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 1262:1395) REMARK 3 ORIGIN FOR THE GROUP (A): 37.6221 -18.1879 -0.6569 REMARK 3 T TENSOR REMARK 3 T11: 0.2742 T22: 0.2518 REMARK 3 T33: 0.2272 T12: 0.0450 REMARK 3 T13: -0.0215 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 1.2205 L22: 0.4318 REMARK 3 L33: 0.7909 L12: -0.1041 REMARK 3 L13: 0.5120 L23: -0.0783 REMARK 3 S TENSOR REMARK 3 S11: 0.0938 S12: 0.2727 S13: 0.1851 REMARK 3 S21: 0.0497 S22: -0.1373 S23: -0.0171 REMARK 3 S31: 0.3518 S32: 0.1216 S33: 0.0015 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 3AVS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000029756. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-10 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 : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : DOUBLE SI(111) CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH 8.5), 0.2M LI2SO4, REMARK 280 18-20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, 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 39.43600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.46150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.43950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.46150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.43600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.43950 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 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 LEU A 908 REMARK 465 SER A 909 REMARK 465 GLU A 1049 REMARK 465 GLU A 1050 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 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 ALA A 1393 O HOH A 322 2.13 REMARK 500 O HOH A 168 O HOH A 232 2.16 REMARK 500 OE2 GLU A 1326 O HOH A 215 2.18 REMARK 500 O HOH A 221 O HOH A 226 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 PRO A 927 152.89 -49.85 REMARK 500 GLU A 946 -45.95 -130.52 REMARK 500 ALA A1008 -123.39 48.24 REMARK 500 MET A1129 -61.89 -104.73 REMARK 500 ILE A1333 -61.02 -95.35 REMARK 500 ASP A1340 -37.83 79.29 REMARK 500 TYR A1354 65.17 38.25 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 NI A1503 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 276 O REMARK 620 2 HIS A1146 NE2 90.6 REMARK 620 3 GLU A1148 OE2 87.9 94.8 REMARK 620 4 HIS A1226 NE2 168.6 86.0 81.6 REMARK 620 5 OGA A1501 O2 90.3 170.1 95.1 94.9 REMARK 620 6 OGA A1501 O2' 88.6 92.7 171.8 102.4 77.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1331 SG REMARK 620 2 CYS A1334 SG 111.3 REMARK 620 3 CYS A1358 SG 112.5 110.0 REMARK 620 4 CYS A1361 SG 106.5 112.0 104.4 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 OGA A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 1505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 1506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1510 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1511 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1512 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1513 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1514 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1515 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1516 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3AVR RELATED DB: PDB REMARK 900 THE H3-BOUND STRUCTURE DBREF 3AVS A 880 1401 UNP O15550 KDM6A_HUMAN 880 1401 SEQADV 3AVS GLY A 871 UNP O15550 EXPRESSION TAG SEQADV 3AVS PRO A 872 UNP O15550 EXPRESSION TAG SEQADV 3AVS GLY A 873 UNP O15550 EXPRESSION TAG SEQADV 3AVS TYR A 874 UNP O15550 EXPRESSION TAG SEQADV 3AVS GLN A 875 UNP O15550 EXPRESSION TAG SEQADV 3AVS ASP A 876 UNP O15550 EXPRESSION TAG SEQADV 3AVS PRO A 877 UNP O15550 EXPRESSION TAG SEQADV 3AVS ASN A 878 UNP O15550 EXPRESSION TAG SEQADV 3AVS SER A 879 UNP O15550 EXPRESSION TAG 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 OGA A1501 13 HET ZN A1502 1 HET NI A1503 1 HET NI A1504 1 HET NI A1505 1 HET CL A1506 1 HET EDO A1507 10 HET EDO A1508 10 HET EDO A1509 10 HET EDO A1510 10 HET EDO A1511 10 HET EDO A1512 10 HET EDO A1513 10 HET EDO A1514 10 HET EDO A1515 10 HET EDO A1516 10 HETNAM OGA N-OXALYLGLYCINE HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 OGA C4 H5 N O5 FORMUL 3 ZN ZN 2+ FORMUL 4 NI 3(NI 2+) FORMUL 7 CL CL 1- FORMUL 8 EDO 10(C2 H6 O2) FORMUL 18 HOH *344(H2 O) HELIX 1 1 SER A 892 ARG A 901 1 10 HELIX 2 2 PRO A 932 LEU A 936 5 5 HELIX 3 3 ASN A 947 PHE A 952 1 6 HELIX 4 4 PRO A 954 ASN A 962 1 9 HELIX 5 5 GLY A 972 LYS A 978 1 7 HELIX 6 6 ASP A 980 PHE A 984 5 5 HELIX 7 7 SER A 985 ASN A 994 1 10 HELIX 8 8 ILE A 1032 LEU A 1047 1 16 HELIX 9 9 TRP A 1096 LEU A 1103 1 8 HELIX 10 10 THR A 1104 LEU A 1106 5 3 HELIX 11 11 PRO A 1107 ARG A 1111 5 5 HELIX 12 12 ASN A 1117 VAL A 1122 5 6 HELIX 13 13 GLU A 1148 PHE A 1152 5 5 HELIX 14 14 PRO A 1170 GLY A 1172 5 3 HELIX 15 15 TYR A 1173 ASN A 1184 1 12 HELIX 16 16 ASN A 1196 ALA A 1203 1 8 HELIX 17 17 THR A 1245 GLN A 1262 1 18 HELIX 18 18 PRO A 1269 ILE A 1281 1 13 HELIX 19 19 ASP A 1285 ALA A 1313 1 29 HELIX 20 20 ASN A 1346 ARG A 1351 1 6 HELIX 21 21 CYS A 1358 SER A 1366 1 9 HELIX 22 22 LYS A 1379 PHE A 1390 1 12 SHEET 1 A 9 SER A 942 TYR A 944 0 SHEET 2 A 9 VAL A 967 ARG A 971 1 O ARG A 971 N ILE A 943 SHEET 3 A 9 LEU A1217 ILE A1220 -1 O LEU A1217 N ILE A 970 SHEET 4 A 9 CYS A1153 PRO A1161 -1 N ASN A1156 O VAL A1218 SHEET 5 A 9 CYS A1234 VAL A1241 -1 O ASN A1235 N ILE A1159 SHEET 6 A 9 GLN A1133 LYS A1137 -1 N TYR A1135 O ASN A1236 SHEET 7 A 9 THR A1081 ASP A1089 -1 N GLY A1085 O MET A1136 SHEET 8 A 9 MET A 997 LEU A1004 -1 N GLU A 999 O THR A1086 SHEET 9 A 9 ASN A1026 THR A1031 -1 O SER A1028 N VAL A1000 SHEET 1 B 4 ARG A1142 HIS A1146 0 SHEET 2 B 4 VAL A1225 ALA A1230 -1 O VAL A1228 N THR A1143 SHEET 3 B 4 CYS A1164 VAL A1169 -1 N GLU A1165 O GLN A1229 SHEET 4 B 4 TYR A1208 GLN A1212 -1 O GLN A1212 N CYS A1164 SHEET 1 C 3 ILE A1318 TRP A1319 0 SHEET 2 C 3 PHE A1372 GLU A1376 1 O GLU A1376 N ILE A1318 SHEET 3 C 3 LEU A1341 THR A1345 -1 N VAL A1344 O VAL A1373 SHEET 1 D 2 HIS A1329 TYR A1330 0 SHEET 2 D 2 GLU A1337 VAL A1338 -1 O VAL A1338 N HIS A1329 LINK O HOH A 276 NI NI A1503 1555 1555 2.20 LINK NE2 HIS A1146 NI NI A1503 1555 1555 2.24 LINK OE2 GLU A1148 NI NI A1503 1555 1555 2.11 LINK NE2 HIS A1226 NI NI A1503 1555 1555 2.19 LINK NE2 HIS A1320 NI NI A1504 1555 1555 2.74 LINK SG CYS A1331 ZN ZN A1502 1555 1555 2.39 LINK SG CYS A1334 ZN ZN A1502 1555 1555 2.38 LINK SG CYS A1358 ZN ZN A1502 1555 1555 2.31 LINK SG CYS A1361 ZN ZN A1502 1555 1555 2.43 LINK O2 OGA A1501 NI NI A1503 1555 1555 2.24 LINK O2' OGA A1501 NI NI A1503 1555 1555 2.24 CISPEP 1 TYR A 928 PRO A 929 0 2.42 CISPEP 2 GLY A 1160 PRO A 1161 0 4.31 SITE 1 AC1 11 HOH A 7 LYS A1137 THR A1143 HIS A1146 SITE 2 AC1 11 GLU A1148 SER A1154 ASN A1156 TRP A1166 SITE 3 AC1 11 HIS A1226 ALA A1238 NI A1503 SITE 1 AC2 4 CYS A1331 CYS A1334 CYS A1358 CYS A1361 SITE 1 AC3 5 HOH A 276 HIS A1146 GLU A1148 HIS A1226 SITE 2 AC3 5 OGA A1501 SITE 1 AC4 2 HOH A 215 HIS A1320 SITE 1 AC5 1 HIS A1101 SITE 1 AC6 1 ARG A1027 SITE 1 AC7 2 HOH A 233 HIS A1121 SITE 1 AC8 4 VAL A1253 GLU A1257 CYS A1295 ARG A1298 SITE 1 AC9 2 TYR A 928 EDO A1510 SITE 1 BC1 6 HOH A 317 THR A1030 LYS A1034 TYR A1035 SITE 2 BC1 6 LYS A1083 EDO A1509 SITE 1 BC2 4 HOH A 35 HOH A 211 ARG A1213 PRO A1214 SITE 1 BC3 3 HOH A 176 HOH A 306 GLU A 946 SITE 1 BC4 6 HOH A 190 LEU A 981 GLY A 982 SER A 985 SITE 2 BC4 6 ILE A1159 EDO A1514 SITE 1 BC5 10 HOH A 107 HOH A 278 SER A 985 THR A 986 SITE 2 BC5 10 GLN A1039 GLY A1160 PRO A1161 CYS A1234 SITE 3 BC5 10 ASN A1235 EDO A1513 SITE 1 BC6 7 HOH A 12 HOH A 84 HOH A 165 HOH A 219 SITE 2 BC6 7 ILE A 889 PRO A 891 ARG A 971 SITE 1 BC7 5 HOH A 309 ALA A1108 ARG A1111 SER A1114 SITE 2 BC7 5 ALA A1115 CRYST1 78.872 82.879 92.923 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 0.012679 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010762 0.00000