HEADER OXIDOREDUCTASE 30-MAR-18 6G5X TITLE CRYSTAL STRUCTURE OF KDM4A WITH COMPOUND YP-02-145 CAVEAT 6G5X MY7 B 406 ATOM C7 IS PLANAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: JMJD2A; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 7 EC: 1.14.11.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS KDM4A, LIGAND BINDING, DRUG DESIGN, INHIBITOR DESIGN, CANCER, KEYWDS 2 EPIGENETICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.H.MALECKI,D.M.CARTER,U.GOHLKE,E.SPECKER,M.NAZARE,M.S.WEISS, AUTHOR 2 U.HEINEMANN REVDAT 3 31-JAN-24 6G5X 1 REMARK REVDAT 2 21-DEC-22 6G5X 1 JRNL LINK REVDAT 1 10-APR-19 6G5X 0 JRNL AUTH D.M.CARTER,E.SPECKER,P.H.MALECKI,J.PRZYGODDA,K.DUDANIEC, JRNL AUTH 2 M.S.WEISS,U.HEINEMANN,M.NAZARE,U.GOHLKE JRNL TITL ENHANCED PROPERTIES OF A BENZIMIDAZOLE BENZYLPYRAZOLE LYSINE JRNL TITL 2 DEMETHYLASE INHIBITOR: MECHANISM-OF-ACTION, BINDING SITE JRNL TITL 3 ANALYSIS, AND ACTIVITY IN CELLULAR MODELS OF PROSTATE JRNL TITL 4 CANCER. JRNL REF J.MED.CHEM. V. 64 14266 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 34555281 JRNL DOI 10.1021/ACS.JMEDCHEM.1C00693 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 81213 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.590 REMARK 3 FREE R VALUE TEST SET COUNT : 2100 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 46.8565 - 4.3877 0.99 5570 149 0.1508 0.1778 REMARK 3 2 4.3877 - 3.4830 1.00 5408 143 0.1376 0.1544 REMARK 3 3 3.4830 - 3.0428 1.00 5343 142 0.1603 0.2014 REMARK 3 4 3.0428 - 2.7646 1.00 5308 141 0.1725 0.2037 REMARK 3 5 2.7646 - 2.5665 1.00 5253 139 0.1737 0.2197 REMARK 3 6 2.5665 - 2.4152 1.00 5303 141 0.1708 0.2045 REMARK 3 7 2.4152 - 2.2942 1.00 5239 139 0.1777 0.2204 REMARK 3 8 2.2942 - 2.1944 1.00 5253 139 0.1799 0.2099 REMARK 3 9 2.1944 - 2.1099 1.00 5248 140 0.1885 0.2626 REMARK 3 10 2.1099 - 2.0371 1.00 5211 138 0.2008 0.2216 REMARK 3 11 2.0371 - 1.9734 1.00 5265 139 0.2168 0.2653 REMARK 3 12 1.9734 - 1.9170 1.00 5214 139 0.2313 0.2928 REMARK 3 13 1.9170 - 1.8665 1.00 5241 139 0.2508 0.2829 REMARK 3 14 1.8665 - 1.8210 1.00 5196 138 0.2642 0.3137 REMARK 3 15 1.8210 - 1.7796 0.97 5061 134 0.2912 0.3267 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.58 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 34.1027 37.8547 18.3969 REMARK 3 T TENSOR REMARK 3 T11: 0.1847 T22: 0.1989 REMARK 3 T33: 0.1673 T12: -0.0098 REMARK 3 T13: 0.0128 T23: 0.0530 REMARK 3 L TENSOR REMARK 3 L11: 0.5744 L22: 1.0408 REMARK 3 L33: 0.7163 L12: 0.1476 REMARK 3 L13: 0.0361 L23: 0.6325 REMARK 3 S TENSOR REMARK 3 S11: 0.0388 S12: 0.0420 S13: 0.0522 REMARK 3 S21: -0.1379 S22: -0.0208 S23: 0.0143 REMARK 3 S31: -0.1158 S32: -0.0128 S33: -0.0098 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 6G5X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81224 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 46.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 5.891 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.91 REMARK 200 R MERGE FOR SHELL (I) : 0.96000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 3PDQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM CITRATE, 10MM NICL2, 20% PEG REMARK 280 3350, PH 5.5, VAPOR DIFFUSION, TEMPERATURE 277K 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 49.56850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.30750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 49.56850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.30750 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 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 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 MET A 1 REMARK 465 ALA A 2 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 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 PRO B 10 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 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 ASP A 311 CB - CG - OD1 ANGL. DEV. = 5.5 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 ALA A 69 59.04 -141.84 REMARK 500 SER A 112 -76.89 -111.00 REMARK 500 ASN A 128 70.85 41.98 REMARK 500 ARG A 152 73.83 -156.78 REMARK 500 MET A 192 16.96 57.23 REMARK 500 ALA A 236 55.36 -149.51 REMARK 500 ARG A 309 -2.56 71.98 REMARK 500 ASN B 128 70.93 42.49 REMARK 500 ARG B 152 66.86 -159.02 REMARK 500 VAL B 171 -65.18 -104.35 REMARK 500 LYS B 182 -3.63 79.64 REMARK 500 MET B 192 17.46 56.90 REMARK 500 ALA B 236 55.05 -147.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 765 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH B 766 DISTANCE = 7.32 ANGSTROMS REMARK 525 HOH B 767 DISTANCE = 8.10 ANGSTROMS REMARK 525 HOH B 768 DISTANCE = 8.85 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 404 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 188 NE2 REMARK 620 2 GLU A 190 OE1 96.5 REMARK 620 3 HIS A 276 NE2 86.9 88.0 REMARK 620 4 CIT A 407 O4 89.7 171.1 98.7 REMARK 620 5 HOH A 506 O 173.1 88.8 97.6 84.5 REMARK 620 6 HOH A 588 O 88.3 87.6 173.0 86.2 87.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 403 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 215 NE2 REMARK 620 2 HOH A 724 O 99.5 REMARK 620 3 HOH A 742 O 93.3 122.8 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 234 SG REMARK 620 2 HIS A 240 NE2 111.4 REMARK 620 3 CYS A 306 SG 111.4 114.2 REMARK 620 4 CYS A 308 SG 116.9 95.3 106.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CIT A 408 O2 REMARK 620 2 CIT A 408 O5 86.9 REMARK 620 3 CIT A 408 O7 87.9 78.7 REMARK 620 4 HOH A 668 O 89.1 163.2 84.8 REMARK 620 5 MY7 B 406 N18 94.4 96.1 174.3 100.5 REMARK 620 6 MY7 B 406 N9 148.6 86.0 120.5 105.4 56.1 REMARK 620 7 MY7 B 406 N10 176.2 93.8 95.9 91.1 81.8 28.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 188 NE2 REMARK 620 2 GLU B 190 OE1 100.5 REMARK 620 3 HIS B 276 NE2 87.3 88.7 REMARK 620 4 CIT B 405 O4 85.6 172.6 95.9 REMARK 620 5 HOH B 503 O 171.7 83.9 99.9 89.5 REMARK 620 6 HOH B 580 O 89.8 87.9 175.1 87.9 83.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 234 SG REMARK 620 2 HIS B 240 NE2 114.6 REMARK 620 3 CYS B 306 SG 114.1 110.2 REMARK 620 4 CYS B 308 SG 118.9 92.0 104.6 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CIT B 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MY7 B 406 DBREF 6G5X A 1 359 UNP O75164 KDM4A_HUMAN 1 359 DBREF 6G5X B 1 359 UNP O75164 KDM4A_HUMAN 1 359 SEQRES 1 A 359 MET ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG SEQRES 2 A 359 ILE MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN SEQRES 3 A 359 PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA SEQRES 4 A 359 HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU SEQRES 5 A 359 TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU SEQRES 6 A 359 VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SEQRES 7 A 359 SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA SEQRES 8 A 359 MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP SEQRES 9 A 359 LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU SEQRES 10 A 359 GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO SEQRES 11 A 359 ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS SEQRES 12 A 359 HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE SEQRES 13 A 359 LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU SEQRES 14 A 359 GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS SEQRES 15 A 359 THR SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SEQRES 16 A 359 SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP SEQRES 17 A 359 TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG SEQRES 18 A 359 LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS SEQRES 19 A 359 GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO SEQRES 20 A 359 LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL SEQRES 21 A 359 THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR SEQRES 22 A 359 GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA SEQRES 23 A 359 GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR SEQRES 24 A 359 GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET SEQRES 25 A 359 VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN SEQRES 26 A 359 PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN SEQRES 27 A 359 THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA ALA SEQRES 28 A 359 GLU PHE LEU LYS GLU SER GLU LEU SEQRES 1 B 359 MET ALA SER GLU SER GLU THR LEU ASN PRO SER ALA ARG SEQRES 2 B 359 ILE MET THR PHE TYR PRO THR MET GLU GLU PHE ARG ASN SEQRES 3 B 359 PHE SER ARG TYR ILE ALA TYR ILE GLU SER GLN GLY ALA SEQRES 4 B 359 HIS ARG ALA GLY LEU ALA LYS VAL VAL PRO PRO LYS GLU SEQRES 5 B 359 TRP LYS PRO ARG ALA SER TYR ASP ASP ILE ASP ASP LEU SEQRES 6 B 359 VAL ILE PRO ALA PRO ILE GLN GLN LEU VAL THR GLY GLN SEQRES 7 B 359 SER GLY LEU PHE THR GLN TYR ASN ILE GLN LYS LYS ALA SEQRES 8 B 359 MET THR VAL ARG GLU PHE ARG LYS ILE ALA ASN SER ASP SEQRES 9 B 359 LYS TYR CYS THR PRO ARG TYR SER GLU PHE GLU GLU LEU SEQRES 10 B 359 GLU ARG LYS TYR TRP LYS ASN LEU THR PHE ASN PRO PRO SEQRES 11 B 359 ILE TYR GLY ALA ASP VAL ASN GLY THR LEU TYR GLU LYS SEQRES 12 B 359 HIS VAL ASP GLU TRP ASN ILE GLY ARG LEU ARG THR ILE SEQRES 13 B 359 LEU ASP LEU VAL GLU LYS GLU SER GLY ILE THR ILE GLU SEQRES 14 B 359 GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS SEQRES 15 B 359 THR SER PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SEQRES 16 B 359 SER ILE ASN TYR LEU HIS PHE GLY GLU PRO LYS SER TRP SEQRES 17 B 359 TYR SER VAL PRO PRO GLU HIS GLY LYS ARG LEU GLU ARG SEQRES 18 B 359 LEU ALA LYS GLY PHE PHE PRO GLY SER ALA GLN SER CYS SEQRES 19 B 359 GLU ALA PHE LEU ARG HIS LYS MET THR LEU ILE SER PRO SEQRES 20 B 359 LEU MET LEU LYS LYS TYR GLY ILE PRO PHE ASP LYS VAL SEQRES 21 B 359 THR GLN GLU ALA GLY GLU PHE MET ILE THR PHE PRO TYR SEQRES 22 B 359 GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA SEQRES 23 B 359 GLU SER THR ASN PHE ALA THR ARG ARG TRP ILE GLU TYR SEQRES 24 B 359 GLY LYS GLN ALA VAL LEU CYS SER CYS ARG LYS ASP MET SEQRES 25 B 359 VAL LYS ILE SER MET ASP VAL PHE VAL ARG LYS PHE GLN SEQRES 26 B 359 PRO GLU ARG TYR LYS LEU TRP LYS ALA GLY LYS ASP ASN SEQRES 27 B 359 THR VAL ILE ASP HIS THR LEU PRO THR PRO GLU ALA ALA SEQRES 28 B 359 GLU PHE LEU LYS GLU SER GLU LEU HET ZN A 401 1 HET NI A 402 1 HET NI A 403 1 HET NI A 404 1 HET EDO A 405 4 HET EDO A 406 4 HET CIT A 407 13 HET CIT A 408 13 HET GOL A 409 6 HET ZN B 401 1 HET NI B 402 1 HET EDO B 403 4 HET EDO B 404 4 HET CIT B 405 13 HET MY7 B 406 25 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CIT CITRIC ACID HETNAM GOL GLYCEROL HETNAM MY7 2-(3-METHYL-5-OXIDANYLIDENE-4-PHENYL-4~{H}-PYRAZOL-1- HETNAM 2 MY7 YL)-3~{H}-BENZIMIDAZOLE-5-CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ZN 2(ZN 2+) FORMUL 4 NI 4(NI 2+) FORMUL 7 EDO 4(C2 H6 O2) FORMUL 9 CIT 3(C6 H8 O7) FORMUL 11 GOL C3 H8 O3 FORMUL 17 MY7 C18 H14 N4 O3 FORMUL 18 HOH *551(H2 O) HELIX 1 AA1 SER A 3 LEU A 8 1 6 HELIX 2 AA2 THR A 20 ARG A 25 1 6 HELIX 3 AA3 ASN A 26 GLN A 37 1 12 HELIX 4 AA4 GLY A 38 ALA A 42 5 5 HELIX 5 AA5 VAL A 94 SER A 103 1 10 HELIX 6 AA6 GLU A 113 LEU A 125 1 13 HELIX 7 AA7 THR A 155 LEU A 157 5 3 HELIX 8 AA8 ASP A 158 GLY A 165 1 8 HELIX 9 AA9 GLU A 190 LEU A 194 5 5 HELIX 10 AB1 PRO A 212 GLU A 214 5 3 HELIX 11 AB2 HIS A 215 PHE A 227 1 13 HELIX 12 AB3 PHE A 227 CYS A 234 1 8 HELIX 13 AB4 ALA A 236 LYS A 241 5 6 HELIX 14 AB5 SER A 246 TYR A 253 1 8 HELIX 15 AB6 ARG A 295 ALA A 303 1 9 HELIX 16 AB7 MET A 317 GLN A 325 1 9 HELIX 17 AB8 ARG A 328 ALA A 334 1 7 HELIX 18 AB9 THR A 347 PHE A 353 5 7 HELIX 19 AC1 THR B 20 ARG B 25 1 6 HELIX 20 AC2 ASN B 26 GLN B 37 1 12 HELIX 21 AC3 GLY B 38 ALA B 42 5 5 HELIX 22 AC4 VAL B 94 SER B 103 1 10 HELIX 23 AC5 GLU B 113 LEU B 125 1 13 HELIX 24 AC6 THR B 155 LEU B 157 5 3 HELIX 25 AC7 ASP B 158 GLY B 165 1 8 HELIX 26 AC8 GLU B 190 LEU B 194 5 5 HELIX 27 AC9 PRO B 212 GLU B 214 5 3 HELIX 28 AD1 HIS B 215 PHE B 227 1 13 HELIX 29 AD2 PHE B 227 CYS B 234 1 8 HELIX 30 AD3 ALA B 236 LYS B 241 5 6 HELIX 31 AD4 SER B 246 TYR B 253 1 8 HELIX 32 AD5 ARG B 295 ALA B 303 1 9 HELIX 33 AD6 MET B 317 GLN B 325 1 9 HELIX 34 AD7 ARG B 328 ALA B 334 1 7 HELIX 35 AD8 THR B 347 LEU B 354 5 8 SHEET 1 AA110 THR A 16 PHE A 17 0 SHEET 2 AA110 LEU A 44 VAL A 47 1 O LYS A 46 N PHE A 17 SHEET 3 AA110 PHE A 267 THR A 270 -1 O ILE A 269 N ALA A 45 SHEET 4 AA110 TYR A 195 GLY A 203 -1 N ASN A 198 O MET A 268 SHEET 5 AA110 ASN A 284 PHE A 291 -1 O GLU A 287 N TYR A 199 SHEET 6 AA110 TYR A 175 GLY A 179 -1 N TYR A 177 O ALA A 286 SHEET 7 AA110 ILE A 131 ASN A 137 -1 N GLY A 133 O PHE A 178 SHEET 8 AA110 ILE A 71 GLN A 78 -1 N ILE A 71 O TYR A 132 SHEET 9 AA110 LEU A 81 GLN A 88 -1 O TYR A 85 N LEU A 74 SHEET 10 AA110 THR A 243 ILE A 245 -1 O LEU A 244 N PHE A 82 SHEET 1 AA2 2 VAL A 66 ILE A 67 0 SHEET 2 AA2 2 MET A 92 THR A 93 -1 O MET A 92 N ILE A 67 SHEET 1 AA3 4 SER A 184 HIS A 188 0 SHEET 2 AA3 4 TYR A 275 ASN A 280 -1 O GLY A 278 N PHE A 185 SHEET 3 AA3 4 LYS A 206 VAL A 211 -1 N SER A 207 O PHE A 279 SHEET 4 AA3 4 ASP A 258 GLN A 262 -1 O GLN A 262 N LYS A 206 SHEET 1 AA410 THR B 16 PHE B 17 0 SHEET 2 AA410 LEU B 44 VAL B 47 1 O LYS B 46 N PHE B 17 SHEET 3 AA410 PHE B 267 THR B 270 -1 O ILE B 269 N ALA B 45 SHEET 4 AA410 TYR B 195 GLY B 203 -1 N ASN B 198 O MET B 268 SHEET 5 AA410 ASN B 284 PHE B 291 -1 O GLU B 287 N TYR B 199 SHEET 6 AA410 TYR B 175 GLY B 179 -1 N TYR B 177 O ALA B 286 SHEET 7 AA410 ILE B 131 ASN B 137 -1 N VAL B 136 O LEU B 176 SHEET 8 AA410 ILE B 71 GLN B 78 -1 N ILE B 71 O TYR B 132 SHEET 9 AA410 LEU B 81 GLN B 88 -1 O TYR B 85 N LEU B 74 SHEET 10 AA410 THR B 243 ILE B 245 -1 O LEU B 244 N PHE B 82 SHEET 1 AA5 2 VAL B 66 ILE B 67 0 SHEET 2 AA5 2 MET B 92 THR B 93 -1 O MET B 92 N ILE B 67 SHEET 1 AA6 4 SER B 184 HIS B 188 0 SHEET 2 AA6 4 TYR B 275 ASN B 280 -1 O GLY B 278 N PHE B 185 SHEET 3 AA6 4 LYS B 206 VAL B 211 -1 N TYR B 209 O ALA B 277 SHEET 4 AA6 4 ASP B 258 GLN B 262 -1 O VAL B 260 N TRP B 208 LINK NE2 HIS A 188 NI NI A 404 1555 1555 2.10 LINK OE1 GLU A 190 NI NI A 404 1555 1555 2.07 LINK NE2 HIS A 215 NI NI A 403 1555 1555 2.36 LINK SG CYS A 234 ZN ZN A 401 1555 1555 2.32 LINK NE2 HIS A 240 ZN ZN A 401 1555 1555 2.05 LINK NE2 HIS A 276 NI NI A 404 1555 1555 2.13 LINK SG CYS A 306 ZN ZN A 401 1555 1555 2.24 LINK SG CYS A 308 ZN ZN A 401 1555 1555 2.35 LINK NI NI A 402 O2 CIT A 408 1555 1555 2.24 LINK NI NI A 402 O5 CIT A 408 1555 1555 2.01 LINK NI NI A 402 O7 CIT A 408 1555 1555 2.15 LINK NI NI A 402 O HOH A 668 1555 1555 2.18 LINK NI NI A 402 N18 MY7 B 406 1555 1555 2.09 LINK NI NI A 402 N9 MY7 B 406 1555 1555 2.80 LINK NI NI A 402 N10 MY7 B 406 1555 1555 2.21 LINK NI NI A 403 O HOH A 724 1555 1555 2.35 LINK NI NI A 403 O HOH A 742 1555 1555 2.57 LINK NI NI A 404 O4 CIT A 407 1555 1555 2.18 LINK NI NI A 404 O HOH A 506 1555 1555 2.26 LINK NI NI A 404 O HOH A 588 1555 1555 2.21 LINK NE2 HIS B 188 NI NI B 402 1555 1555 2.15 LINK OE1 GLU B 190 NI NI B 402 1555 1555 2.05 LINK SG CYS B 234 ZN ZN B 401 1555 1555 2.23 LINK NE2 HIS B 240 ZN ZN B 401 1555 1555 2.14 LINK NE2 HIS B 276 NI NI B 402 1555 1555 2.13 LINK SG CYS B 306 ZN ZN B 401 1555 1555 2.33 LINK SG CYS B 308 ZN ZN B 401 1555 1555 2.31 LINK NI NI B 402 O4 CIT B 405 1555 1555 2.15 LINK NI NI B 402 O HOH B 503 1555 1555 2.10 LINK NI NI B 402 O HOH B 580 1555 1555 2.16 SITE 1 AC1 4 CYS A 234 HIS A 240 CYS A 306 CYS A 308 SITE 1 AC2 3 CIT A 408 HOH A 668 MY7 B 406 SITE 1 AC3 3 HIS A 215 HOH A 724 HOH A 742 SITE 1 AC4 6 HIS A 188 GLU A 190 HIS A 276 CIT A 407 SITE 2 AC4 6 HOH A 506 HOH A 588 SITE 1 AC5 6 GLU A 235 ALA A 236 PHE A 237 LEU A 238 SITE 2 AC5 6 HOH A 510 HOH A 519 SITE 1 AC6 4 ARG A 98 ASN A 102 HOH A 680 HOH B 709 SITE 1 AC7 17 TYR A 132 TYR A 177 PHE A 185 HIS A 188 SITE 2 AC7 17 ASN A 198 LYS A 206 TRP A 208 HIS A 276 SITE 3 AC7 17 ALA A 286 SER A 288 NI A 404 HOH A 506 SITE 4 AC7 17 HOH A 570 HOH A 588 HOH A 597 HOH A 624 SITE 5 AC7 17 HOH A 646 SITE 1 AC8 9 GLU A 214 HIS A 215 ARG A 218 NI A 402 SITE 2 AC8 9 HOH A 514 HOH A 668 GLU B 115 LYS B 259 SITE 3 AC8 9 MY7 B 406 SITE 1 AC9 6 SER A 316 ASP A 318 ARG A 322 LYS A 330 SITE 2 AC9 6 HOH A 512 HOH A 657 SITE 1 AD1 4 CYS B 234 HIS B 240 CYS B 306 CYS B 308 SITE 1 AD2 6 HIS B 188 GLU B 190 HIS B 276 CIT B 405 SITE 2 AD2 6 HOH B 503 HOH B 580 SITE 1 AD3 6 LYS B 224 GLU B 235 ALA B 236 PHE B 237 SITE 2 AD3 6 LEU B 238 EDO B 404 SITE 1 AD4 7 HIS B 188 THR B 189 LEU B 238 ARG B 239 SITE 2 AD4 7 TYR B 275 EDO B 403 HOH B 593 SITE 1 AD5 16 TYR B 132 TYR B 177 PHE B 185 HIS B 188 SITE 2 AD5 16 ASN B 198 LYS B 206 TRP B 208 HIS B 276 SITE 3 AD5 16 ALA B 286 NI B 402 HOH B 503 HOH B 550 SITE 4 AD5 16 HOH B 580 HOH B 615 HOH B 659 HOH B 675 SITE 1 AD6 19 HIS A 215 ARG A 218 GLY A 254 PRO A 256 SITE 2 AD6 19 NI A 402 CIT A 408 PHE B 114 GLU B 115 SITE 3 AD6 19 GLU B 118 SER B 207 TRP B 208 TYR B 209 SITE 4 AD6 19 LYS B 259 VAL B 260 THR B 261 HOH B 583 SITE 5 AD6 19 HOH B 619 HOH B 644 HOH B 658 CRYST1 99.137 148.615 56.910 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 0.010087 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006729 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017572 0.00000