HEADER OXIDOREDUCTASE 27-OCT-17 6ETV TITLE CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLHYDRAZIDE COMPOUND 2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2D; COMPND 6 EC: 1.14.11.-; COMPND 7 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, TETRAZOLYLHYDRAZIDE, TETRAZOLE, INHIBITOR KEYWDS 2 DESIGN, CANCER, EPIGENETICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN REVDAT 3 17-JAN-24 6ETV 1 REMARK LINK REVDAT 2 11-MAR-20 6ETV 1 JRNL REVDAT 1 27-FEB-19 6ETV 0 JRNL AUTH P.H.MALECKI,N.RUGER,M.ROATSCH,O.KRYLOVA,A.LINK,M.JUNG, JRNL AUTH 2 U.HEINEMANN,M.S.WEISS JRNL TITL STRUCTURE-BASED SCREENING OF TETRAZOLYLHYDRAZIDE INHIBITORS JRNL TITL 2 VERSUS KDM4 HISTONE DEMETHYLASES. JRNL REF CHEMMEDCHEM V. 14 1828 2019 JRNL REFN ESSN 1860-7187 JRNL PMID 31475772 JRNL DOI 10.1002/CMDC.201900441 REMARK 2 REMARK 2 RESOLUTION. 1.18 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 247114 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2582 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 47.9581 - 3.0811 1.00 13610 145 0.1241 0.1480 REMARK 3 2 3.0811 - 2.4456 1.00 13631 140 0.1135 0.1665 REMARK 3 3 2.4456 - 2.1364 1.00 13642 140 0.1070 0.1413 REMARK 3 4 2.1364 - 1.9411 1.00 13563 144 0.1009 0.1082 REMARK 3 5 1.9411 - 1.8020 1.00 13633 148 0.0967 0.1306 REMARK 3 6 1.8020 - 1.6957 1.00 13605 142 0.1001 0.1152 REMARK 3 7 1.6957 - 1.6108 1.00 13648 144 0.1009 0.1391 REMARK 3 8 1.6108 - 1.5407 1.00 13603 145 0.1008 0.1317 REMARK 3 9 1.5407 - 1.4814 1.00 13593 142 0.1094 0.1272 REMARK 3 10 1.4814 - 1.4302 1.00 13627 147 0.1204 0.1598 REMARK 3 11 1.4302 - 1.3855 1.00 13586 143 0.1348 0.1831 REMARK 3 12 1.3855 - 1.3459 1.00 13609 141 0.1485 0.1863 REMARK 3 13 1.3459 - 1.3105 1.00 13651 146 0.1545 0.1846 REMARK 3 14 1.3105 - 1.2785 1.00 13602 146 0.1668 0.1783 REMARK 3 15 1.2785 - 1.2494 1.00 13576 143 0.1772 0.2189 REMARK 3 16 1.2494 - 1.2228 1.00 13657 143 0.1873 0.1904 REMARK 3 17 1.2228 - 1.1984 1.00 13616 145 0.2059 0.2103 REMARK 3 18 1.1984 - 1.1758 0.96 13080 138 0.2298 0.2352 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.15 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 : 0.024 3284 REMARK 3 ANGLE : 2.216 4509 REMARK 3 CHIRALITY : 0.145 452 REMARK 3 PLANARITY : 0.013 596 REMARK 3 DIHEDRAL : 15.055 1314 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 6ETV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1200007234. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-OCT-16 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 : X-AREA REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 247119 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 47.918 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.762 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.48 REMARK 200 R MERGE FOR SHELL (I) : 0.87800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.010 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 (%): 51.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 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 75.22200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.74500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.74500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.83300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.74500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.74500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.61100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.74500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.74500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.83300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.74500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.74500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.61100 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 75.22200 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: 2380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 846 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 865 LIES ON A SPECIAL POSITION. 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: 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 NI NI A 412 HAK BXE A 413 1.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 80 CB SER A 80 OG -0.098 REMARK 500 GLU A 208 CD GLU A 208 OE1 -0.076 REMARK 500 ASN A 294 N ASN A 294 CA 0.172 REMARK 500 PHE A 324 CG PHE A 324 CD1 -0.097 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 82 CG - CD - NE ANGL. DEV. = -13.9 DEGREES REMARK 500 ARG A 82 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 MET A 96 CG - SD - CE ANGL. DEV. = -10.1 DEGREES REMARK 500 ILE A 135 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 MET A 196 CG - SD - CE ANGL. DEV. = 12.9 DEGREES REMARK 500 ASN A 294 CB - CA - C ANGL. DEV. = 16.6 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 LYS A 186 -7.75 75.86 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 970 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH A 971 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH A 972 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 973 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH A 974 DISTANCE = 6.74 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 NA A 403 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 17 OD1 REMARK 620 2 HOH A 612 O 47.8 REMARK 620 3 HOH A 650 O 74.6 28.6 REMARK 620 4 HOH A 836 O 93.2 59.5 35.9 REMARK 620 5 HOH A 846 O 87.2 64.2 46.6 15.7 REMARK 620 6 HOH A 846 O 85.6 63.7 47.0 17.3 1.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 412 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 100.4 REMARK 620 3 HIS A 280 NE2 86.9 86.4 REMARK 620 4 BXE A 413 OAI 90.7 168.8 94.1 REMARK 620 5 BXE A 413 NAK 169.4 90.1 95.3 78.7 REMARK 620 6 HOH A 589 O 89.4 91.5 175.3 88.9 88.9 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 109.0 REMARK 620 3 CYS A 310 SG 116.8 109.9 REMARK 620 4 CYS A 312 SG 113.8 99.1 106.8 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 NA 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 EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 SO4 A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BXE A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 415 DBREF 6ETV 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 NA A 403 1 HET EDO A 404 10 HET EDO A 405 10 HET EDO A 406 10 HET EDO A 407 10 HET EDO A 408 10 HET EDO A 409 20 HET EDO A 410 10 HET SO4 A 411 5 HET NI A 412 1 HET BXE A 413 20 HET GOL A 414 27 HET EPE A 415 32 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION HETNAM BXE [3-(2~{H}-1,2,3,4-TETRAZOL-5-YL)PROPANOYLAMINO]AZANIUM HETNAM GOL GLYCEROL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EPE HEPES FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 NA NA 1+ FORMUL 5 EDO 7(C2 H6 O2) FORMUL 12 SO4 O4 S 2- FORMUL 13 NI NI 2+ FORMUL 14 BXE C4 H9 N6 O 1+ FORMUL 15 GOL C3 H8 O3 FORMUL 16 EPE C8 H18 N2 O4 S FORMUL 17 HOH *474(H2 O) HELIX 1 AA1 ASP A 30 GLN A 41 1 12 HELIX 2 AA2 GLY A 42 ALA A 46 5 5 HELIX 3 AA3 VAL A 98 ASN A 106 1 9 HELIX 4 AA4 ASN A 117 ARG A 129 1 13 HELIX 5 AA5 ILE A 130 ASN A 132 5 3 HELIX 6 AA6 THR A 159 GLY A 169 1 11 HELIX 7 AA7 GLU A 194 LEU A 198 5 5 HELIX 8 AA8 PRO A 216 GLU A 218 5 3 HELIX 9 AA9 HIS A 219 PHE A 231 1 13 HELIX 10 AB1 PHE A 231 CYS A 238 1 8 HELIX 11 AB2 ALA A 240 LYS A 245 5 6 HELIX 12 AB3 SER A 250 ASN A 257 1 8 HELIX 13 AB4 ARG A 299 ALA A 307 1 9 HELIX 14 AB5 PHE A 319 GLN A 329 1 11 HELIX 15 AB6 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 179 O ALA A 292 SHEET 7 AA110 ILE A 135 SER A 141 -1 N GLY A 137 O PHE A 182 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 OD1 ASN A 17 NA NA A 403 1555 8554 2.41 LINK NE2 HIS A 192 NI NI A 412 1555 1555 2.05 LINK OE2 GLU A 194 NI NI A 412 1555 1555 1.96 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.30 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.04 LINK NE2 HIS A 280 NI NI A 412 1555 1555 2.13 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.26 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.32 LINK NA NA A 403 O HOH A 612 1555 1555 2.40 LINK NA NA A 403 O HOH A 650 1555 8554 2.23 LINK NA NA A 403 O AHOH A 836 1555 1555 2.31 LINK NA NA A 403 O HOH A 846 1555 1555 2.33 LINK NA NA A 403 O HOH A 846 1555 8554 2.36 LINK NI NI A 412 OAI BXE A 413 1555 1555 2.03 LINK NI NI A 412 NAK BXE A 413 1555 1555 2.08 LINK NI NI A 412 O HOH A 589 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 6 ASN A 17 ASN A 262 HOH A 612 HOH A 650 SITE 2 AC3 6 HOH A 836 HOH A 846 SITE 1 AC4 5 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 2 AC4 5 HOH A 826 SITE 1 AC5 7 LYS A 150 GLN A 151 TRP A 152 ASN A 153 SITE 2 AC5 7 HIS A 156 HOH A 598 HOH A 716 SITE 1 AC6 3 THR A 252 ARG A 263 HOH A 696 SITE 1 AC7 6 LYS A 109 GLN A 111 ASN A 132 TRP A 185 SITE 2 AC7 6 LYS A 186 HOH A 515 SITE 1 AC8 7 SER A 80 THR A 87 CYS A 168 LYS A 305 SITE 2 AC8 7 HOH A 516 HOH A 529 HOH A 924 SITE 1 AC9 5 PHE A 118 ARG A 263 ILE A 264 THR A 265 SITE 2 AC9 5 HOH A 570 SITE 1 AD1 5 GLU A 27 TYR A 37 HOH A 548 HOH A 667 SITE 2 AD1 5 HOH A 860 SITE 1 AD2 9 ARG A 60 GLU A 61 THR A 62 ASN A 65 SITE 2 AD2 9 HOH A 531 HOH A 534 HOH A 549 HOH A 798 SITE 3 AD2 9 HOH A 822 SITE 1 AD3 5 HIS A 192 GLU A 194 HIS A 280 BXE A 413 SITE 2 AD3 5 HOH A 589 SITE 1 AD4 13 TYR A 136 TYR A 181 HIS A 192 GLU A 194 SITE 2 AD4 13 SER A 200 ASN A 202 LYS A 210 HIS A 280 SITE 3 AD4 13 NI A 412 HOH A 503 HOH A 554 HOH A 589 SITE 4 AD4 13 HOH A 712 SITE 1 AD5 6 ARG A 102 HIS A 103 ASN A 106 HOH A 596 SITE 2 AD5 6 HOH A 662 HOH A 829 SITE 1 AD6 20 MET A 19 ILE A 20 TYR A 37 GLN A 41 SITE 2 AD6 20 LYS A 255 GLU A 256 HOH A 511 HOH A 533 SITE 3 AD6 20 HOH A 573 HOH A 579 HOH A 654 HOH A 825 SITE 4 AD6 20 HOH A 878 HOH A 898 HOH A 911 HOH A 930 SITE 5 AD6 20 HOH A 953 HOH A 970 HOH A 971 HOH A 974 CRYST1 71.490 71.490 150.444 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 0.013988 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013988 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006647 0.00000