HEADER OXIDOREDUCTASE 02-DEC-17 6F5T TITLE CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLE LIGAND GF057 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 6F5T 1 LINK REVDAT 1 12-DEC-18 6F5T 0 JRNL AUTH P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLE LIGAND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.58 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.880 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 103813 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2101 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 48.4293 - 3.8960 0.97 6709 142 0.1531 0.1708 REMARK 3 2 3.8960 - 3.0925 0.96 6610 135 0.1449 0.1608 REMARK 3 3 3.0925 - 2.7016 0.99 6805 139 0.1542 0.1494 REMARK 3 4 2.7016 - 2.4546 1.00 6849 141 0.1490 0.2118 REMARK 3 5 2.4546 - 2.2787 0.97 6700 138 0.1583 0.1513 REMARK 3 6 2.2787 - 2.1443 0.98 6784 138 0.1844 0.2279 REMARK 3 7 2.1443 - 2.0370 0.99 6801 144 0.1762 0.2103 REMARK 3 8 2.0370 - 1.9483 0.99 6854 137 0.2014 0.2192 REMARK 3 9 1.9483 - 1.8733 0.99 6825 140 0.2652 0.2851 REMARK 3 10 1.8733 - 1.8086 0.98 6735 140 0.2369 0.2928 REMARK 3 11 1.8086 - 1.7521 0.99 6853 143 0.2608 0.3117 REMARK 3 12 1.7521 - 1.7020 1.00 6828 140 0.2813 0.2804 REMARK 3 13 1.7020 - 1.6572 1.00 6879 142 0.3141 0.3369 REMARK 3 14 1.6572 - 1.6168 1.00 6855 143 0.3383 0.3305 REMARK 3 15 1.6168 - 1.5800 0.96 6625 139 0.4768 0.4080 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.620 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.88 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 : 0.015 2946 REMARK 3 ANGLE : 1.339 4003 REMARK 3 CHIRALITY : 0.074 391 REMARK 3 PLANARITY : 0.010 517 REMARK 3 DIHEDRAL : 15.667 1750 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3141 -1.5168 -18.6034 REMARK 3 T TENSOR REMARK 3 T11: 0.1729 T22: 0.2339 REMARK 3 T33: 0.2197 T12: 0.0079 REMARK 3 T13: 0.0273 T23: -0.0321 REMARK 3 L TENSOR REMARK 3 L11: 0.9243 L22: 2.6691 REMARK 3 L33: 1.6183 L12: 0.2227 REMARK 3 L13: 0.2563 L23: -0.5216 REMARK 3 S TENSOR REMARK 3 S11: -0.1166 S12: 0.0151 S13: 0.1018 REMARK 3 S21: 0.1822 S22: 0.0498 S23: -0.3115 REMARK 3 S31: -0.2009 S32: 0.2425 S33: 0.0834 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1603 -23.6936 -23.1407 REMARK 3 T TENSOR REMARK 3 T11: 0.2322 T22: 0.1732 REMARK 3 T33: 0.2396 T12: 0.0082 REMARK 3 T13: 0.0262 T23: -0.0288 REMARK 3 L TENSOR REMARK 3 L11: 2.5677 L22: 2.1114 REMARK 3 L33: 3.4125 L12: -0.7631 REMARK 3 L13: 2.0141 L23: -0.1681 REMARK 3 S TENSOR REMARK 3 S11: 0.0123 S12: 0.1347 S13: -0.1693 REMARK 3 S21: -0.0068 S22: 0.0057 S23: -0.1735 REMARK 3 S31: 0.2940 S32: 0.2289 S33: -0.0288 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): -2.0299 -5.5319 -10.4028 REMARK 3 T TENSOR REMARK 3 T11: 0.2342 T22: 0.2341 REMARK 3 T33: 0.2066 T12: 0.0265 REMARK 3 T13: -0.0128 T23: -0.0036 REMARK 3 L TENSOR REMARK 3 L11: 0.8383 L22: 1.0978 REMARK 3 L33: 0.7686 L12: -0.8412 REMARK 3 L13: -0.2969 L23: -0.0106 REMARK 3 S TENSOR REMARK 3 S11: -0.1573 S12: -0.1168 S13: 0.0926 REMARK 3 S21: 0.2744 S22: 0.1434 S23: -0.0880 REMARK 3 S31: -0.0298 S32: 0.0620 S33: 0.0129 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 297 ) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3387 -7.5965 -24.7524 REMARK 3 T TENSOR REMARK 3 T11: 0.1480 T22: 0.1523 REMARK 3 T33: 0.1448 T12: -0.0149 REMARK 3 T13: 0.0285 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 0.8729 L22: 1.6824 REMARK 3 L33: 2.1887 L12: 0.0924 REMARK 3 L13: 0.7125 L23: 0.7650 REMARK 3 S TENSOR REMARK 3 S11: -0.0441 S12: 0.0284 S13: -0.0248 REMARK 3 S21: -0.0100 S22: -0.0002 S23: 0.0963 REMARK 3 S31: 0.0631 S32: -0.0998 S33: 0.0465 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 298 THROUGH 320 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.2573 -0.6785 -14.2704 REMARK 3 T TENSOR REMARK 3 T11: 0.2924 T22: 0.2265 REMARK 3 T33: 0.2330 T12: 0.0159 REMARK 3 T13: 0.0066 T23: 0.0285 REMARK 3 L TENSOR REMARK 3 L11: 4.2507 L22: 3.9331 REMARK 3 L33: 2.1619 L12: 3.0389 REMARK 3 L13: 0.9468 L23: 2.7033 REMARK 3 S TENSOR REMARK 3 S11: 0.2115 S12: -0.1738 S13: -0.4745 REMARK 3 S21: 0.7437 S22: -0.3379 S23: -0.2281 REMARK 3 S31: 0.4018 S32: -0.1343 S33: 0.1891 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 321 THROUGH 340 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0992 -0.5171 -9.2120 REMARK 3 T TENSOR REMARK 3 T11: 0.2114 T22: 0.2251 REMARK 3 T33: 0.1807 T12: 0.0055 REMARK 3 T13: 0.0622 T23: 0.0175 REMARK 3 L TENSOR REMARK 3 L11: 3.0494 L22: 5.9823 REMARK 3 L33: 4.0775 L12: -0.5719 REMARK 3 L13: 1.4112 L23: 0.8744 REMARK 3 S TENSOR REMARK 3 S11: -0.2664 S12: -0.1863 S13: -0.2769 REMARK 3 S21: 0.3663 S22: 0.1539 S23: 0.2559 REMARK 3 S31: 0.1896 S32: -0.3188 S33: 0.1343 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 6F5T 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_1200007788. 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 : 104082 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 48.407 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.822 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.84 REMARK 200 R MERGE FOR SHELL (I) : 2.73000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.510 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: 4ETS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 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 76.03900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.10650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.10650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 114.05850 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.10650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.10650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.01950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.10650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.10650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 114.05850 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.10650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.10650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.01950 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 76.03900 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: 2260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 770 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 811 LIES ON A SPECIAL POSITION. 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 -5.97 76.70 REMARK 500 MET A 196 19.74 56.11 REMARK 500 CYS A 238 117.62 -168.54 REMARK 500 ALA A 240 40.43 -88.50 REMARK 500 PHE A 319 3.00 -64.32 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 A 406 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 97.6 REMARK 620 3 HIS A 280 NE2 87.6 87.5 REMARK 620 4 CQK A 407 NAI 98.6 160.8 103.6 REMARK 620 5 CQK A 407 NAO 84.6 96.9 171.5 74.3 REMARK 620 6 HOH A 544 O 174.3 87.4 89.8 77.1 97.7 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 110.2 REMARK 620 3 CYS A 310 SG 115.5 109.5 REMARK 620 4 CYS A 312 SG 117.0 96.5 106.4 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CQK A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 DBREF 6F5T A 11 340 UNP Q6B0I6 KDM4D_HUMAN 11 340 SEQRES 1 A 330 ALA GLN ASN PRO ASN CYS ASN ILE MET ILE PHE HIS PRO SEQRES 2 A 330 THR LYS GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA SEQRES 3 A 330 TYR MET GLU SER GLN GLY ALA HIS ARG ALA GLY LEU ALA SEQRES 4 A 330 LYS ILE ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU THR SEQRES 5 A 330 TYR ASP ASN ILE SER GLU ILE LEU ILE ALA THR PRO LEU SEQRES 6 A 330 GLN GLN VAL ALA SER GLY ARG ALA GLY VAL PHE THR GLN SEQRES 7 A 330 TYR HIS LYS LYS LYS LYS ALA MET THR VAL GLY GLU TYR SEQRES 8 A 330 ARG HIS LEU ALA ASN SER LYS LYS TYR GLN THR PRO PRO SEQRES 9 A 330 HIS GLN ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS SEQRES 10 A 330 ASN ARG ILE TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SEQRES 11 A 330 SER GLY SER LEU PHE ASP GLU ASN THR LYS GLN TRP ASN SEQRES 12 A 330 LEU GLY HIS LEU GLY THR ILE GLN ASP LEU LEU GLU LYS SEQRES 13 A 330 GLU CYS GLY VAL VAL ILE GLU GLY VAL ASN THR PRO TYR SEQRES 14 A 330 LEU TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS SEQRES 15 A 330 THR GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS SEQRES 16 A 330 LEU GLY GLU PRO LYS THR TRP TYR VAL VAL PRO PRO GLU SEQRES 17 A 330 HIS GLY GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE SEQRES 18 A 330 PRO GLY SER SER ARG GLY CYS GLY ALA PHE LEU ARG HIS SEQRES 19 A 330 LYS VAL ALA LEU ILE SER PRO THR VAL LEU LYS GLU ASN SEQRES 20 A 330 GLY ILE PRO PHE ASN ARG ILE THR GLN GLU ALA GLY GLU SEQRES 21 A 330 PHE MET VAL THR PHE PRO TYR GLY TYR HIS ALA GLY PHE SEQRES 22 A 330 ASN HIS GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA SEQRES 23 A 330 THR PRO ARG TRP ILE ASP TYR GLY LYS MET ALA SER GLN SEQRES 24 A 330 CYS SER CYS GLY GLU ALA ARG VAL THR PHE SER MET ASP SEQRES 25 A 330 ALA PHE VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU SEQRES 26 A 330 TRP LYS ARG GLY GLN HET ZN A 401 1 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET NI A 406 1 HET CQK A 407 15 HET EPE A 408 15 HET EPE A 409 15 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION HETNAM CQK ~{N}-OXIDANYL-4-(2~{H}-1,2,3,4-TETRAZOL-5-YL)PYRIDINE- HETNAM 2 CQK 2-CARBOXAMIDE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EPE HEPES HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 NI NI 2+ FORMUL 8 CQK C7 H6 N6 O2 FORMUL 9 EPE 2(C8 H18 N2 O4 S) FORMUL 11 EDO 3(C2 H6 O2) FORMUL 14 HOH *324(H2 O) HELIX 1 AA1 LYS A 25 ASN A 29 5 5 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 HIS A 280 N HIS A 192 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 ILE A 264 N TRP A 212 LINK NE2 HIS A 192 NI NI A 406 1555 1555 2.16 LINK OE2 GLU A 194 NI NI A 406 1555 1555 2.08 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.26 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.16 LINK NE2 HIS A 280 NI NI A 406 1555 1555 2.19 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.24 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.31 LINK NI NI A 406 NAI CQK A 407 1555 1555 2.17 LINK NI NI A 406 NAO CQK A 407 1555 1555 2.15 LINK NI NI A 406 O HOH A 544 1555 1555 2.14 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 5 ARG A 102 HIS A 103 ASN A 106 HOH A 501 SITE 2 AC2 5 HOH A 507 SITE 1 AC3 5 ASN A 65 ILE A 66 SER A 67 ARG A 102 SITE 2 AC3 5 HOH A 643 SITE 1 AC4 6 PRO A 113 LYS A 124 ASN A 128 TRP A 185 SITE 2 AC4 6 LYS A 186 HOH A 608 SITE 1 AC5 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 1 AC6 5 HIS A 192 GLU A 194 HIS A 280 CQK A 407 SITE 2 AC6 5 HOH A 544 SITE 1 AC7 15 TYR A 136 TYR A 181 PHE A 189 HIS A 192 SITE 2 AC7 15 GLU A 194 LYS A 210 TRP A 212 LYS A 245 SITE 3 AC7 15 HIS A 280 NI A 406 HOH A 518 HOH A 544 SITE 4 AC7 15 HOH A 605 HOH A 652 HOH A 720 SITE 1 AC8 14 PHE A 21 HIS A 22 TYR A 34 TYR A 37 SITE 2 AC8 14 GLN A 41 GLU A 256 GLY A 258 EPE A 409 SITE 3 AC8 14 HOH A 513 HOH A 586 HOH A 612 HOH A 666 SITE 4 AC8 14 HOH A 787 HOH A 795 SITE 1 AC9 6 GLU A 27 LYS A 33 TYR A 34 TYR A 37 SITE 2 AC9 6 EPE A 408 HOH A 589 SITE 1 AD1 3 MET A 306 HOH A 531 HOH A 786 SITE 1 AD2 3 ARG A 263 ILE A 264 THR A 265 SITE 1 AD3 6 PHE A 28 ASP A 30 PHE A 31 GLN A 151 SITE 2 AD3 6 TRP A 152 HOH A 746 CRYST1 72.213 72.213 152.078 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 0.013848 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013848 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006576 0.00000