HEADER OXIDOREDUCTASE 02-DEC-17 6F5S TITLE CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLE LIGAND GF049 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: JMJD2D; COMPND 5 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 6 JUMONJI DOMAIN-CONTAINING PROTEIN 2D; 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: KDM4D, JHDM3D, JMJD2D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS KDM4D, LIGAND BINDING, LIGAND OPTIMIZATION, DRUG DEVELOPMENT, KEYWDS 2 TETRAZOLE, INHIBITOR DESIGN, CANCER, EPIGENETICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN REVDAT 2 17-JAN-24 6F5S 1 REMARK LINK REVDAT 1 12-DEC-18 6F5S 0 JRNL AUTH P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLE LIGAND GF049 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.48 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) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.900 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 128720 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.630 REMARK 3 FREE R VALUE TEST SET COUNT : 2094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.4633 - 3.6396 1.00 8457 144 0.1341 0.1443 REMARK 3 2 3.6396 - 2.8890 1.00 8503 136 0.1407 0.1556 REMARK 3 3 2.8890 - 2.5238 1.00 8477 144 0.1424 0.1799 REMARK 3 4 2.5238 - 2.2931 1.00 8514 137 0.1389 0.1721 REMARK 3 5 2.2931 - 2.1287 1.00 8431 137 0.1398 0.1630 REMARK 3 6 2.1287 - 2.0032 1.00 8523 142 0.1545 0.2080 REMARK 3 7 2.0032 - 1.9029 1.00 8486 142 0.1652 0.1624 REMARK 3 8 1.9029 - 1.8200 1.00 8493 141 0.1770 0.1842 REMARK 3 9 1.8200 - 1.7500 1.00 8466 146 0.2019 0.2137 REMARK 3 10 1.7500 - 1.6896 1.00 8514 138 0.2255 0.3077 REMARK 3 11 1.6896 - 1.6367 1.00 8499 140 0.2733 0.3155 REMARK 3 12 1.6367 - 1.5900 1.00 8484 140 0.2916 0.3864 REMARK 3 13 1.5900 - 1.5481 1.00 8476 137 0.3094 0.3419 REMARK 3 14 1.5481 - 1.5103 1.00 8467 143 0.3360 0.3436 REMARK 3 15 1.5103 - 1.4780 0.92 7836 127 0.3665 0.3622 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.41 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 2971 REMARK 3 ANGLE : 1.029 4044 REMARK 3 CHIRALITY : 0.083 399 REMARK 3 PLANARITY : 0.007 530 REMARK 3 DIHEDRAL : 17.457 1126 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.8738 -1.8053 -18.9194 REMARK 3 T TENSOR REMARK 3 T11: 0.1606 T22: 0.2331 REMARK 3 T33: 0.2088 T12: -0.0083 REMARK 3 T13: 0.0285 T23: -0.0252 REMARK 3 L TENSOR REMARK 3 L11: 0.7515 L22: 2.1825 REMARK 3 L33: 1.6227 L12: 0.1679 REMARK 3 L13: -0.0129 L23: -0.2223 REMARK 3 S TENSOR REMARK 3 S11: -0.0623 S12: 0.0080 S13: 0.0890 REMARK 3 S21: 0.0940 S22: 0.0580 S23: -0.2242 REMARK 3 S31: -0.1962 S32: 0.2454 S33: 0.0445 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.2385 -23.5016 -23.2192 REMARK 3 T TENSOR REMARK 3 T11: 0.1854 T22: 0.1134 REMARK 3 T33: 0.2049 T12: -0.0051 REMARK 3 T13: 0.0458 T23: -0.0297 REMARK 3 L TENSOR REMARK 3 L11: 3.0662 L22: 2.1161 REMARK 3 L33: 4.4843 L12: -1.0503 REMARK 3 L13: 2.0904 L23: -0.4233 REMARK 3 S TENSOR REMARK 3 S11: -0.0271 S12: 0.1121 S13: -0.1955 REMARK 3 S21: -0.0148 S22: 0.0226 S23: -0.1059 REMARK 3 S31: 0.2319 S32: 0.1737 S33: 0.0005 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0003 -5.1741 -10.3135 REMARK 3 T TENSOR REMARK 3 T11: 0.1944 T22: 0.2262 REMARK 3 T33: 0.1818 T12: 0.0155 REMARK 3 T13: 0.0059 T23: -0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.6065 L22: 1.6353 REMARK 3 L33: 1.0832 L12: -0.4363 REMARK 3 L13: -0.0615 L23: 0.2888 REMARK 3 S TENSOR REMARK 3 S11: -0.1227 S12: -0.0709 S13: 0.0218 REMARK 3 S21: 0.1535 S22: 0.1230 S23: -0.0466 REMARK 3 S31: -0.0331 S32: 0.0314 S33: 0.0037 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.7815 -5.9753 -24.1384 REMARK 3 T TENSOR REMARK 3 T11: 0.1590 T22: 0.1678 REMARK 3 T33: 0.1573 T12: -0.0177 REMARK 3 T13: 0.0245 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.5326 L22: 1.1314 REMARK 3 L33: 1.3928 L12: 0.0162 REMARK 3 L13: 0.2234 L23: 0.6666 REMARK 3 S TENSOR REMARK 3 S11: -0.0457 S12: 0.0564 S13: 0.0210 REMARK 3 S21: -0.0443 S22: 0.0087 S23: 0.0536 REMARK 3 S31: 0.0219 S32: -0.0644 S33: 0.0451 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 307 THROUGH 340 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.3706 -2.6026 -9.9361 REMARK 3 T TENSOR REMARK 3 T11: 0.3147 T22: 0.2251 REMARK 3 T33: 0.2599 T12: 0.0173 REMARK 3 T13: 0.0398 T23: 0.0269 REMARK 3 L TENSOR REMARK 3 L11: 5.5081 L22: 7.4243 REMARK 3 L33: 7.5291 L12: 4.8077 REMARK 3 L13: 0.7118 L23: 4.6521 REMARK 3 S TENSOR REMARK 3 S11: -0.0327 S12: -0.1021 S13: -0.6176 REMARK 3 S21: 0.5757 S22: -0.0874 S23: -0.2000 REMARK 3 S31: 0.9240 S32: -0.1054 S33: 0.1230 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 6F5S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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 : 128737 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 48.437 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.723 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.27 REMARK 200 R MERGE FOR SHELL (I) : 2.57100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.540 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: 6ETS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES, 180MM AMMONIUM SULPHATE, REMARK 280 24% PEG 3350, PH 7, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 76.13150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.12700 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.12700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 114.19725 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.12700 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.12700 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.06575 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.12700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.12700 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 114.19725 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.12700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.12700 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.06575 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 76.13150 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 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -48.0 KCAL/MOL 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 MET A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 ASN A 9 REMARK 465 CYS A 10 REMARK 465 ASP A 341 REMARK 465 ARG A 342 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 LYS A 186 -7.43 79.34 REMARK 500 MET A 196 19.20 59.01 REMARK 500 ALA A 240 42.27 -96.03 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 A 871 DISTANCE = 6.45 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 411 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 98.6 REMARK 620 3 HIS A 280 NE2 86.7 88.8 REMARK 620 4 CQT A 412 NAO 95.7 162.5 102.1 REMARK 620 5 CQT A 412 OAH 83.7 94.2 170.3 77.4 REMARK 620 6 HOH A 553 O 173.0 88.3 92.7 77.6 96.6 REMARK 620 N 1 2 3 4 5 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 238 SG REMARK 620 2 HIS A 244 NE2 108.6 REMARK 620 3 CYS A 310 SG 116.5 111.0 REMARK 620 4 CYS A 312 SG 114.6 99.2 105.6 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 CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CQT A 412 DBREF 6F5S A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342 SEQRES 1 A 342 MET GLU THR MET LYS SER LYS ALA ASN CYS ALA GLN ASN SEQRES 2 A 342 PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR LYS GLU SEQRES 3 A 342 GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR MET GLU SEQRES 4 A 342 SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE ILE SEQRES 5 A 342 PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR ASP ASN SEQRES 6 A 342 ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN GLN VAL SEQRES 7 A 342 ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR HIS LYS SEQRES 8 A 342 LYS LYS LYS ALA MET THR VAL GLY GLU TYR ARG HIS LEU SEQRES 9 A 342 ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS GLN ASN SEQRES 10 A 342 PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN ARG ILE SEQRES 11 A 342 TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER GLY SER SEQRES 12 A 342 LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU GLY HIS SEQRES 13 A 342 LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU CYS GLY SEQRES 14 A 342 VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE SEQRES 15 A 342 GLY MET TRP LYS THR THR PHE ALA TRP HIS THR GLU ASP SEQRES 16 A 342 MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU GLY GLU SEQRES 17 A 342 PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS GLY GLN SEQRES 18 A 342 ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO GLY SER SEQRES 19 A 342 SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS VAL ALA SEQRES 20 A 342 LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY ILE PRO SEQRES 21 A 342 PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE MET VAL SEQRES 22 A 342 THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY SEQRES 23 A 342 PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR PRO ARG SEQRES 24 A 342 TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SER CYS SEQRES 25 A 342 GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA PHE VAL SEQRES 26 A 342 ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP LYS ARG SEQRES 27 A 342 GLY GLN ASP ARG HET ZN A 401 1 HET CL A 402 1 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET SO4 A 408 5 HET SO4 A 409 5 HET SO4 A 410 5 HET NI A 411 1 HET CQT A 412 23 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION HETNAM CQT ~{N}-(3-MORPHOLIN-4-YLPROPYL)-4-(2~{H}-1,2,3,4- HETNAM 2 CQT TETRAZOL-5-YL)PYRIDINE-2-CARBOXAMIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 EDO 5(C2 H6 O2) FORMUL 9 SO4 3(O4 S 2-) FORMUL 12 NI NI 2+ FORMUL 13 CQT C14 H19 N7 O2 FORMUL 14 HOH *371(H2 O) HELIX 1 AA1 GLU A 26 ASN A 29 5 4 HELIX 2 AA2 ASP A 30 GLN A 41 1 12 HELIX 3 AA3 GLY A 42 ALA A 46 5 5 HELIX 4 AA4 ASN A 65 GLU A 68 5 4 HELIX 5 AA5 VAL A 98 ASN A 106 1 9 HELIX 6 AA6 ASN A 117 ARG A 129 1 13 HELIX 7 AA7 ILE A 130 ASN A 132 5 3 HELIX 8 AA8 THR A 159 GLY A 169 1 11 HELIX 9 AA9 GLU A 194 LEU A 198 5 5 HELIX 10 AB1 PRO A 216 GLU A 218 5 3 HELIX 11 AB2 HIS A 219 PHE A 231 1 13 HELIX 12 AB3 PHE A 231 CYS A 238 1 8 HELIX 13 AB4 ALA A 240 LYS A 245 5 6 HELIX 14 AB5 SER A 250 ASN A 257 1 8 HELIX 15 AB6 ARG A 299 ALA A 307 1 9 HELIX 16 AB7 SER A 320 GLN A 329 1 10 HELIX 17 AB8 GLN A 329 GLN A 340 1 12 SHEET 1 AA110 MET A 19 PHE A 21 0 SHEET 2 AA110 LEU A 48 ILE A 51 1 O LYS A 50 N PHE A 21 SHEET 3 AA110 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA110 TYR A 199 GLY A 207 -1 N ASN A 202 O MET A 272 SHEET 5 AA110 ASN A 288 PHE A 295 -1 O GLU A 291 N TYR A 203 SHEET 6 AA110 TYR A 179 GLY A 183 -1 N TYR A 181 O ALA A 290 SHEET 7 AA110 ILE A 135 SER A 141 -1 N ILE A 140 O LEU A 180 SHEET 8 AA110 LEU A 75 ARG A 82 -1 N LEU A 75 O TYR A 136 SHEET 9 AA110 VAL A 85 LYS A 92 -1 O LYS A 91 N GLN A 76 SHEET 10 AA110 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AA2 2 LEU A 70 ILE A 71 0 SHEET 2 AA2 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AA3 4 THR A 188 HIS A 192 0 SHEET 2 AA3 4 TYR A 279 ASN A 284 -1 O GLY A 282 N PHE A 189 SHEET 3 AA3 4 LYS A 210 VAL A 215 -1 N TYR A 213 O ALA A 281 SHEET 4 AA3 4 ASN A 262 GLN A 266 -1 O GLN A 266 N LYS A 210 LINK NE2 HIS A 192 NI NI A 411 1555 1555 2.12 LINK OE2 GLU A 194 NI NI A 411 1555 1555 2.07 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.30 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.07 LINK NE2 HIS A 280 NI NI A 411 1555 1555 2.18 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.23 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.33 LINK NI NI A 411 NAO CQT A 412 1555 1555 2.15 LINK NI NI A 411 OAH CQT A 412 1555 1555 2.16 LINK NI NI A 411 O HOH A 553 1555 1555 2.13 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 2 ASN A 128 LYS A 186 SITE 1 AC3 4 GLN A 76 LYS A 91 ARG A 332 HOH A 627 SITE 1 AC4 4 HIS A 115 ASN A 117 PHE A 118 HOH A 526 SITE 1 AC5 4 ARG A 263 ILE A 264 THR A 265 HOH A 642 SITE 1 AC6 4 GLU A 218 HIS A 219 ARG A 222 HOH A 663 SITE 1 AC7 6 PHE A 28 ASN A 29 PHE A 31 GLN A 151 SITE 2 AC7 6 TRP A 152 HOH A 501 SITE 1 AC8 6 ARG A 102 HIS A 103 ASN A 106 HOH A 503 SITE 2 AC8 6 HOH A 513 HOH A 516 SITE 1 AC9 5 ASN A 65 ILE A 66 SER A 67 ARG A 102 SITE 2 AC9 5 HOH A 542 SITE 1 AD1 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 1 AD2 5 HIS A 192 GLU A 194 HIS A 280 CQT A 412 SITE 2 AD2 5 HOH A 553 SITE 1 AD3 15 ASP A 139 TYR A 179 TYR A 181 PHE A 189 SITE 2 AD3 15 HIS A 192 GLU A 194 ASP A 195 LYS A 210 SITE 3 AD3 15 LYS A 245 HIS A 280 THR A 318 NI A 411 SITE 4 AD3 15 HOH A 553 HOH A 698 HOH A 763 CRYST1 72.254 72.254 152.263 90.00 90.00 90.00 P 43 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 0.013840 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013840 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006568 0.00000