HEADER OXIDOREDUCTASE 27-JUN-14 4URA TITLE CRYSTAL STRUCTURE OF HUMAN JMJD2A IN COMPLEX WITH COMPOUND 14A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-359; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2A, JMJD2A; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, JUMONJIC, HISTONE DEMETHYLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.KROJER,K.S.ENGLAND,M.VOLLMAR,L.CRAWLEY,E.WILLIAMS,E.RIESEBOS, AUTHOR 2 A.SZYKOWSKA,N.BURGESS-BROWN,U.OPPERMANN,P.E.BRENNAN,C.BOUNTRA, AUTHOR 3 C.H.ARROWSMITH,A.EDWARDS,F.VON DELFT REVDAT 3 24-JAN-18 4URA 1 AUTHOR REVDAT 2 18-JAN-17 4URA 1 JRNL REVDAT 1 17-JUN-15 4URA 0 JRNL AUTH K.S.ENGLAND,A.TUMBER,T.KROJER,G.SCOZZAFAVA,S.S.NG,M.DANIEL, JRNL AUTH 2 A.SZYKOWSKA,K.CHE,F.VON DELFT,N.A.BURGESS-BROWN,A.KAWAMURA, JRNL AUTH 3 C.J.SCHOFIELD,P.E.BRENNAN JRNL TITL OPTIMISATION OF A TRIAZOLOPYRIDINE BASED HISTONE DEMETHYLASE JRNL TITL 2 INHIBITOR YIELDS A POTENT AND SELECTIVE KDM2A (FBXL11) JRNL TITL 3 INHIBITOR. JRNL REF MEDCHEMCOMM V. 5 1879 2014 JRNL REFN ISSN 2040-2503 JRNL PMID 26682034 JRNL DOI 10.1039/C4MD00291A REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 43186 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1821 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 60.1561 - 5.2425 0.97 3307 158 0.1635 0.2113 REMARK 3 2 5.2425 - 4.1614 1.00 3237 165 0.1512 0.1772 REMARK 3 3 4.1614 - 3.6355 1.00 3227 146 0.1829 0.2482 REMARK 3 4 3.6355 - 3.3031 1.00 3238 154 0.2105 0.2713 REMARK 3 5 3.3031 - 3.0664 0.97 3076 129 0.2272 0.3079 REMARK 3 6 3.0664 - 2.8856 1.00 3186 154 0.2370 0.2943 REMARK 3 7 2.8856 - 2.7411 1.00 3183 142 0.2435 0.2882 REMARK 3 8 2.7411 - 2.6217 1.00 3186 126 0.2602 0.3630 REMARK 3 9 2.6217 - 2.5208 1.00 3159 123 0.2753 0.3749 REMARK 3 10 2.5208 - 2.4338 1.00 3191 121 0.2684 0.3388 REMARK 3 11 2.4338 - 2.3577 1.00 3177 132 0.2646 0.3158 REMARK 3 12 2.3577 - 2.2903 0.99 3122 142 0.2736 0.3043 REMARK 3 13 2.2903 - 2.2300 0.97 3076 129 0.2969 0.3522 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) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.62 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 : 0.008 5752 REMARK 3 ANGLE : 1.132 7821 REMARK 3 CHIRALITY : 0.045 813 REMARK 3 PLANARITY : 0.006 1028 REMARK 3 DIHEDRAL : 13.838 2070 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 4URA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1290061107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43239 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 60.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.30 REMARK 200 R MERGE FOR SHELL (I) : 0.83000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM REMARK 280 SULFATE, 11% PEG3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 50.52000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.83000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.52000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.83000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 PHE A 353 REMARK 465 LEU A 354 REMARK 465 LYS A 355 REMARK 465 GLU A 356 REMARK 465 SER A 357 REMARK 465 GLU A 358 REMARK 465 LEU A 359 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 SER B 5 REMARK 465 GLU B 6 REMARK 465 THR B 7 REMARK 465 LEU B 8 REMARK 465 ASN B 9 REMARK 465 LEU B 354 REMARK 465 LYS B 355 REMARK 465 GLU B 356 REMARK 465 SER B 357 REMARK 465 GLU B 358 REMARK 465 LEU B 359 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 GLU A 4 CG CD OE1 OE2 REMARK 470 ARG A 13 NE CZ NH1 NH2 REMARK 470 GLU A 22 CG CD OE1 OE2 REMARK 470 ARG A 25 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 29 CZ NH1 NH2 REMARK 470 LYS A 51 CE NZ REMARK 470 LYS A 54 CG CD CE NZ REMARK 470 ASP A 63 CG OD1 OD2 REMARK 470 LYS A 90 CD CE NZ REMARK 470 ARG A 95 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 99 CG CD CE NZ REMARK 470 ARG A 110 CG CD NE CZ NH1 NH2 REMARK 470 SER A 112 OG REMARK 470 GLU A 113 CD OE1 OE2 REMARK 470 GLU A 115 CD OE1 OE2 REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 ARG A 154 CD NE CZ NH1 NH2 REMARK 470 LYS A 162 CG CD CE NZ REMARK 470 ARG A 221 CD NE CZ NH1 NH2 REMARK 470 LYS A 224 CD CE NZ REMARK 470 GLN A 232 CG CD OE1 NE2 REMARK 470 LYS A 310 CG CD CE NZ REMARK 470 LYS A 330 CD CE NZ REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 GLU B 22 CG CD OE1 OE2 REMARK 470 ARG B 29 CZ NH1 NH2 REMARK 470 LYS B 51 CD CE NZ REMARK 470 LYS B 54 CE NZ REMARK 470 LYS B 90 CG CD CE NZ REMARK 470 LYS B 99 CD CE NZ REMARK 470 ARG B 110 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 113 OE1 OE2 REMARK 470 GLU B 115 CG CD OE1 OE2 REMARK 470 GLU B 142 CG CD OE1 OE2 REMARK 470 LYS B 143 CG CD CE NZ REMARK 470 ARG B 154 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 161 CD OE1 OE2 REMARK 470 LYS B 162 CD CE NZ REMARK 470 GLU B 163 CG CD OE1 OE2 REMARK 470 GLN B 232 CD OE1 NE2 REMARK 470 LYS B 310 CG CD CE NZ REMARK 470 LYS B 323 NZ REMARK 470 ARG B 328 CZ NH1 NH2 REMARK 470 LYS B 333 CD CE NZ REMARK 470 LYS B 336 CG CD CE NZ 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 OG SER B 58 OD1 ASP B 60 2.02 REMARK 500 O GLY A 203 O HOH A 2049 2.09 REMARK 500 O LYS B 89 O HOH B 2014 2.15 REMARK 500 OD1 ASN B 137 O HOH B 2047 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 TYR A 59 33.56 -99.40 REMARK 500 ALA A 69 70.73 -150.71 REMARK 500 ALA A 91 156.93 -49.85 REMARK 500 SER A 112 -93.91 -83.60 REMARK 500 ARG A 152 74.11 -157.79 REMARK 500 VAL A 171 -62.80 -94.55 REMARK 500 MET A 192 18.09 55.95 REMARK 500 ALA A 236 57.28 -147.44 REMARK 500 THR B 20 -178.43 -68.16 REMARK 500 ASP B 61 35.02 -91.86 REMARK 500 ILE B 62 14.24 -140.09 REMARK 500 SER B 103 161.51 -43.06 REMARK 500 SER B 112 -70.32 -102.58 REMARK 500 LYS B 143 -17.14 -49.85 REMARK 500 ARG B 152 70.04 -156.63 REMARK 500 ILE B 156 -8.23 -59.50 REMARK 500 MET B 192 18.59 55.02 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 A2501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEL A4000 N7 REMARK 620 2 LEL A4000 N3 69.8 REMARK 620 3 HIS A 188 NE2 89.9 71.1 REMARK 620 4 HIS A 276 NE2 114.8 163.9 93.1 REMARK 620 5 HOH A2043 O 78.5 102.5 168.3 93.6 REMARK 620 6 GLU A 190 OE2 161.3 100.7 102.5 78.9 88.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 306 SG REMARK 620 2 CYS A 308 SG 110.6 REMARK 620 3 HIS A 240 NE2 118.3 91.8 REMARK 620 4 CYS A 234 SG 115.0 108.8 109.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B2501 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 LEL B4000 N7 90.7 REMARK 620 3 LEL B4000 N3 83.6 74.6 REMARK 620 4 HOH B2062 O 153.4 67.8 104.3 REMARK 620 5 GLU B 190 OE2 113.2 156.1 107.9 88.9 REMARK 620 6 HIS B 276 NE2 84.2 101.5 167.2 85.0 80.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B2502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 110.0 REMARK 620 3 CYS B 308 SG 116.5 89.3 REMARK 620 4 CYS B 306 SG 114.3 113.2 111.1 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 NI A 2501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LEL A 4000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 2501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 2502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LEL B 4000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1353 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1354 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1354 DBREF 4URA A 1 359 UNP O75164 KDM4A_HUMAN 1 359 DBREF 4URA B 1 359 UNP O75164 KDM4A_HUMAN 1 359 SEQADV 4URA SER A 0 UNP O75164 EXPRESSION TAG SEQADV 4URA SER B 0 UNP O75164 EXPRESSION TAG SEQRES 1 A 360 SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER ALA SEQRES 2 A 360 ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE ARG SEQRES 3 A 360 ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY SEQRES 4 A 360 ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS SEQRES 5 A 360 GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP SEQRES 6 A 360 LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY SEQRES 7 A 360 GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS SEQRES 8 A 360 ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER SEQRES 9 A 360 ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU SEQRES 10 A 360 LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO SEQRES 11 A 360 PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU SEQRES 12 A 360 LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR SEQRES 13 A 360 ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE SEQRES 14 A 360 GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP SEQRES 15 A 360 LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU SEQRES 16 A 360 TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER SEQRES 17 A 360 TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU SEQRES 18 A 360 ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER SEQRES 19 A 360 CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER SEQRES 20 A 360 PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS SEQRES 21 A 360 VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO SEQRES 22 A 360 TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS SEQRES 23 A 360 ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU SEQRES 24 A 360 TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP SEQRES 25 A 360 MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE SEQRES 26 A 360 GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP SEQRES 27 A 360 ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA SEQRES 28 A 360 ALA GLU PHE LEU LYS GLU SER GLU LEU SEQRES 1 B 360 SER MET ALA SER GLU SER GLU THR LEU ASN PRO SER ALA SEQRES 2 B 360 ARG ILE MET THR PHE TYR PRO THR MET GLU GLU PHE ARG SEQRES 3 B 360 ASN PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY SEQRES 4 B 360 ALA HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS SEQRES 5 B 360 GLU TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP SEQRES 6 B 360 LEU VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY SEQRES 7 B 360 GLN SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS SEQRES 8 B 360 ALA MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER SEQRES 9 B 360 ASP LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU SEQRES 10 B 360 LEU GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO SEQRES 11 B 360 PRO ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU SEQRES 12 B 360 LYS HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR SEQRES 13 B 360 ILE LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE SEQRES 14 B 360 GLU GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP SEQRES 15 B 360 LYS THR SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU SEQRES 16 B 360 TYR SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER SEQRES 17 B 360 TRP TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU SEQRES 18 B 360 ARG LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER SEQRES 19 B 360 CYS GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER SEQRES 20 B 360 PRO LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS SEQRES 21 B 360 VAL THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO SEQRES 22 B 360 TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS SEQRES 23 B 360 ALA GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU SEQRES 24 B 360 TYR GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP SEQRES 25 B 360 MET VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE SEQRES 26 B 360 GLN PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP SEQRES 27 B 360 ASN THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA SEQRES 28 B 360 ALA GLU PHE LEU LYS GLU SER GLU LEU HET EDO A1353 4 HET SO4 A1354 5 HET NI A2501 1 HET ZN A2502 1 HET LEL A4000 14 HET SO4 B1354 5 HET NI B2501 1 HET ZN B2502 1 HET LEL B4000 14 HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION HETNAM ZN ZINC ION HETNAM LEL 2-(2H-1,2,3-TRIAZOL-4-YL)PYRIDINE-4-CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO C2 H6 O2 FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 NI 2(NI 2+) FORMUL 6 ZN 2(ZN 2+) FORMUL 7 LEL 2(C8 H6 N4 O2) FORMUL 12 HOH *185(H2 O) HELIX 1 1 THR A 20 ARG A 25 1 6 HELIX 2 2 ASN A 26 GLN A 37 1 12 HELIX 3 3 GLY A 38 ALA A 42 5 5 HELIX 4 4 ASP A 61 ASP A 64 5 4 HELIX 5 5 VAL A 94 SER A 103 1 10 HELIX 6 6 GLU A 113 LEU A 125 1 13 HELIX 7 7 THR A 155 LEU A 157 5 3 HELIX 8 8 ASP A 158 GLY A 165 1 8 HELIX 9 9 GLU A 190 LEU A 194 5 5 HELIX 10 10 PRO A 212 GLU A 214 5 3 HELIX 11 11 HIS A 215 PHE A 227 1 13 HELIX 12 12 PHE A 227 CYS A 234 1 8 HELIX 13 13 ALA A 236 LYS A 241 5 6 HELIX 14 14 SER A 246 TYR A 253 1 8 HELIX 15 15 ARG A 295 ALA A 303 1 9 HELIX 16 16 MET A 317 GLN A 325 1 9 HELIX 17 17 ARG A 328 ALA A 334 1 7 HELIX 18 18 THR A 347 GLU A 352 5 6 HELIX 19 19 THR B 20 ARG B 25 1 6 HELIX 20 20 ASN B 26 GLN B 37 1 12 HELIX 21 21 GLY B 38 ALA B 42 5 5 HELIX 22 22 VAL B 94 SER B 103 1 10 HELIX 23 23 GLU B 113 ASN B 124 1 12 HELIX 24 24 THR B 155 GLU B 161 5 7 HELIX 25 25 GLU B 190 LEU B 194 5 5 HELIX 26 26 PRO B 212 GLU B 214 5 3 HELIX 27 27 HIS B 215 PHE B 227 1 13 HELIX 28 28 PHE B 227 CYS B 234 1 8 HELIX 29 29 ALA B 236 LYS B 241 5 6 HELIX 30 30 SER B 246 TYR B 253 1 8 HELIX 31 31 ARG B 295 ALA B 303 1 9 HELIX 32 32 MET B 317 GLN B 325 1 9 HELIX 33 33 ARG B 328 ALA B 334 1 7 HELIX 34 34 THR B 347 ALA B 351 5 5 SHEET 1 AA10 MET A 15 PHE A 17 0 SHEET 2 AA10 LEU A 44 VAL A 47 1 O LEU A 44 N MET A 15 SHEET 3 AA10 PHE A 267 THR A 270 -1 O PHE A 267 N VAL A 47 SHEET 4 AA10 TYR A 195 GLY A 203 -1 O SER A 196 N THR A 270 SHEET 5 AA10 ASN A 284 PHE A 291 -1 O CYS A 285 N HIS A 201 SHEET 6 AA10 TYR A 175 GLY A 179 -1 O TYR A 175 N SER A 288 SHEET 7 AA10 ILE A 131 ASN A 137 -1 O GLY A 133 N PHE A 178 SHEET 8 AA10 ILE A 71 GLN A 78 -1 O ILE A 71 N TYR A 132 SHEET 9 AA10 LEU A 81 GLN A 88 -1 O LEU A 81 N GLN A 78 SHEET 10 AA10 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 AB 2 VAL A 66 ILE A 67 0 SHEET 2 AB 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 AC 4 SER A 184 HIS A 188 0 SHEET 2 AC 4 TYR A 275 ASN A 280 -1 O HIS A 276 N HIS A 188 SHEET 3 AC 4 LYS A 206 VAL A 211 -1 O SER A 207 N PHE A 279 SHEET 4 AC 4 ASP A 258 GLN A 262 -1 O ASP A 258 N SER A 210 SHEET 1 BA10 MET B 15 PHE B 17 0 SHEET 2 BA10 LEU B 44 VAL B 47 1 O LEU B 44 N MET B 15 SHEET 3 BA10 PHE B 267 THR B 270 -1 O PHE B 267 N VAL B 47 SHEET 4 BA10 TYR B 195 GLY B 203 -1 O SER B 196 N THR B 270 SHEET 5 BA10 ASN B 284 PHE B 291 -1 O CYS B 285 N HIS B 201 SHEET 6 BA10 TYR B 175 GLY B 179 -1 O TYR B 175 N SER B 288 SHEET 7 BA10 ILE B 131 ASN B 137 -1 O GLY B 133 N PHE B 178 SHEET 8 BA10 ILE B 71 GLN B 78 -1 O ILE B 71 N TYR B 132 SHEET 9 BA10 LEU B 81 GLN B 88 -1 O LEU B 81 N GLN B 78 SHEET 10 BA10 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 BB 2 VAL B 66 ILE B 67 0 SHEET 2 BB 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 BC 4 SER B 184 HIS B 188 0 SHEET 2 BC 4 TYR B 275 ASN B 280 -1 O HIS B 276 N HIS B 188 SHEET 3 BC 4 LYS B 206 VAL B 211 -1 O SER B 207 N PHE B 279 SHEET 4 BC 4 ASP B 258 GLN B 262 -1 O ASP B 258 N SER B 210 LINK NI NI A2501 N7 LEL A4000 1555 1555 2.43 LINK NI NI A2501 N3 LEL A4000 1555 1555 2.60 LINK NI NI A2501 NE2 HIS A 188 1555 1555 2.53 LINK NI NI A2501 NE2 HIS A 276 1555 1555 2.42 LINK NI NI A2501 O HOH A2043 1555 1555 2.62 LINK NI NI A2501 OE2 GLU A 190 1555 1555 2.41 LINK ZN ZN A2502 SG CYS A 306 1555 1555 2.43 LINK ZN ZN A2502 SG CYS A 308 1555 1555 2.58 LINK ZN ZN A2502 NE2 HIS A 240 1555 1555 2.29 LINK ZN ZN A2502 SG CYS A 234 1555 1555 2.46 LINK NI NI B2501 NE2 HIS B 188 1555 1555 2.48 LINK NI NI B2501 N7 LEL B4000 1555 1555 2.43 LINK NI NI B2501 N3 LEL B4000 1555 1555 2.51 LINK NI NI B2501 O HOH B2062 1555 1555 2.62 LINK NI NI B2501 OE2 GLU B 190 1555 1555 2.42 LINK NI NI B2501 NE2 HIS B 276 1555 1555 2.54 LINK ZN ZN B2502 SG CYS B 234 1555 1555 2.47 LINK ZN ZN B2502 NE2 HIS B 240 1555 1555 2.36 LINK ZN ZN B2502 SG CYS B 308 1555 1555 2.53 LINK ZN ZN B2502 SG CYS B 306 1555 1555 2.43 SITE 1 AC1 5 HIS A 188 GLU A 190 HIS A 276 HOH A2043 SITE 2 AC1 5 LEL A4000 SITE 1 AC2 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC3 10 TYR A 132 TYR A 177 PHE A 185 HIS A 188 SITE 2 AC3 10 GLU A 190 LYS A 206 LYS A 241 EDO A1353 SITE 3 AC3 10 HOH A2085 NI A2501 SITE 1 AC4 5 HIS B 188 GLU B 190 HIS B 276 HOH B2062 SITE 2 AC4 5 LEL B4000 SITE 1 AC5 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AC6 10 TYR B 132 TYR B 177 PHE B 185 HIS B 188 SITE 2 AC6 10 GLU B 190 LYS B 206 TRP B 208 LYS B 241 SITE 3 AC6 10 HOH B2062 NI B2501 SITE 1 AC7 7 GLY A 170 TYR A 177 GLU A 190 SER A 196 SITE 2 AC7 7 SER A 288 HOH A2043 LEL A4000 SITE 1 AC8 5 PHE A 227 PRO A 228 GLY A 229 SER A 230 SITE 2 AC8 5 LYS B 105 SITE 1 AC9 5 LYS A 105 PHE B 227 PRO B 228 GLY B 229 SITE 2 AC9 5 SER B 230 CRYST1 101.040 149.660 57.860 90.00 90.00 90.00 P 21 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 0.009897 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006682 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017283 0.00000