HEADER OXIDOREDUCTASE 27-OCT-17 6ETS TITLE CRYSTAL STRUCTURE OF KDM4D WITH TETRAZOLHYDRAZIDE COMPOUND 1 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, TETRAZOLHYDRAZIDE, 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 6ETS 1 LINK REVDAT 2 11-MAR-20 6ETS 1 JRNL REVDAT 1 20-FEB-19 6ETS 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. 1.33 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 168548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.129 REMARK 3 FREE R VALUE : 0.156 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.240 REMARK 3 FREE R VALUE TEST SET COUNT : 2086 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 32.0436 - 3.2852 0.95 10694 133 0.1243 0.1280 REMARK 3 2 3.2852 - 2.6079 0.97 10962 140 0.1181 0.1473 REMARK 3 3 2.6079 - 2.2784 0.99 11145 141 0.1117 0.1418 REMARK 3 4 2.2784 - 2.0701 0.99 11117 138 0.1073 0.1504 REMARK 3 5 2.0701 - 1.9217 0.98 11126 136 0.1069 0.1394 REMARK 3 6 1.9217 - 1.8084 0.99 11098 139 0.1107 0.1480 REMARK 3 7 1.8084 - 1.7179 0.99 11122 142 0.1165 0.1369 REMARK 3 8 1.7179 - 1.6431 0.99 11207 145 0.1236 0.1590 REMARK 3 9 1.6431 - 1.5798 0.99 11143 142 0.1319 0.1843 REMARK 3 10 1.5798 - 1.5253 0.99 11172 139 0.1488 0.2297 REMARK 3 11 1.5253 - 1.4776 0.99 11207 142 0.1653 0.1846 REMARK 3 12 1.4776 - 1.4354 0.99 11136 134 0.1811 0.2092 REMARK 3 13 1.4354 - 1.3976 0.99 11132 141 0.2029 0.2213 REMARK 3 14 1.3976 - 1.3635 0.99 11206 141 0.2163 0.2266 REMARK 3 15 1.3635 - 1.3325 0.98 10995 133 0.2399 0.2651 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.330 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.54 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 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 : 0.035 3137 REMARK 3 ANGLE : 2.617 4300 REMARK 3 CHIRALITY : 0.195 432 REMARK 3 PLANARITY : 0.016 568 REMARK 3 DIHEDRAL : 14.198 1222 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 6ETS 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_1200007221. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-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 : 14.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.894 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 168562 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 48.014 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.078 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.98 REMARK 200 R MERGE FOR SHELL (I) : 0.75900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.920 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: 4HOO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 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 75.38500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.81550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.81550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.07750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.81550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.81550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.69250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.81550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.81550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.07750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.81550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.81550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.69250 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 75.38500 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: 2860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 829 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 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 HH12 ARG A 82 O HOH A 503 1.51 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 GLU A 39 CD GLU A 39 OE1 -0.071 REMARK 500 LYS A 58 CA LYS A 58 C 0.169 REMARK 500 LYS A 58 CA LYS A 58 C 0.177 REMARK 500 THR A 62 CB THR A 62 CG2 -0.214 REMARK 500 ASN A 65 CA ASN A 65 C 0.233 REMARK 500 ASN A 65 CA ASN A 65 C 0.227 REMARK 500 GLU A 68 CD GLU A 68 OE1 -0.076 REMARK 500 SER A 80 CB SER A 80 OG -0.084 REMARK 500 SER A 80 CB SER A 80 OG -0.113 REMARK 500 ARG A 82 CZ ARG A 82 NH1 -0.078 REMARK 500 ARG A 82 CZ ARG A 82 NH2 -0.089 REMARK 500 HIS A 90 N HIS A 90 CA 0.134 REMARK 500 ARG A 123 CZ ARG A 123 NH2 -0.089 REMARK 500 TYR A 136 CG TYR A 136 CD2 -0.087 REMARK 500 GLU A 165 CD GLU A 165 OE2 -0.073 REMARK 500 ASN A 176 N ASN A 176 CA 0.120 REMARK 500 ASN A 176 CA ASN A 176 C 0.203 REMARK 500 TYR A 181 CE1 TYR A 181 CZ -0.094 REMARK 500 GLU A 208 CD GLU A 208 OE1 -0.080 REMARK 500 GLU A 218 CG GLU A 218 CD 0.095 REMARK 500 GLU A 218 CD GLU A 218 OE1 0.093 REMARK 500 CYS A 289 CA CYS A 289 C 0.184 REMARK 500 ASN A 294 CG ASN A 294 ND2 -0.151 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 TYR A 34 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 ASP A 64 CB - CG - OD2 ANGL. DEV. = -8.1 DEGREES REMARK 500 ASP A 64 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 MET A 96 CG - SD - CE ANGL. DEV. = -10.0 DEGREES REMARK 500 ARG A 102 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 GLN A 111 CG - CD - OE1 ANGL. DEV. = -13.1 DEGREES REMARK 500 ASP A 139 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP A 146 CB - CG - OD1 ANGL. DEV. = 6.6 DEGREES REMARK 500 HIS A 156 O - C - N ANGL. DEV. = -10.0 DEGREES REMARK 500 ASP A 162 CB - CG - OD2 ANGL. DEV. = -7.0 DEGREES REMARK 500 LEU A 164 CB - CG - CD1 ANGL. DEV. = -14.5 DEGREES REMARK 500 ASN A 176 CA - C - O ANGL. DEV. = 14.7 DEGREES REMARK 500 ASN A 176 CA - C - N ANGL. DEV. = -18.0 DEGREES REMARK 500 ASP A 195 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 MET A 196 CG - SD - CE ANGL. DEV. = 15.5 DEGREES REMARK 500 ARG A 222 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 228 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 CYS A 289 CA - CB - SG ANGL. DEV. = 11.3 DEGREES REMARK 500 ARG A 299 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 MET A 321 CG - SD - CE ANGL. DEV. = 12.5 DEGREES REMARK 500 ASP A 322 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 322 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 PHE A 324 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 332 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ASP A 334 CB - CG - OD1 ANGL. DEV. = 7.0 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 -8.51 75.26 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 958 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 959 DISTANCE = 6.89 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 630 O 78.0 REMARK 620 3 HOH A 649 O 51.3 28.4 REMARK 620 4 HOH A 829 O 91.6 48.0 66.2 REMARK 620 5 HOH A 829 O 91.5 48.0 66.2 0.0 REMARK 620 N 1 2 3 4 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 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 100.6 REMARK 620 3 HIS A 280 NE2 86.0 89.3 REMARK 620 4 I1L A 416 OAI 89.3 170.1 90.6 REMARK 620 5 I1L A 416 NAJ 166.3 92.6 98.2 77.6 REMARK 620 6 HOH A 738 O 87.8 91.8 173.8 89.4 87.8 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 108.2 REMARK 620 3 CYS A 310 SG 116.6 109.9 REMARK 620 4 CYS A 312 SG 113.5 99.6 107.7 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 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 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue I1L A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 417 DBREF 6ETS A 1 341 UNP Q6B0I6 KDM4D_HUMAN 1 341 SEQRES 1 A 341 MET GLU THR MET LYS SER LYS ALA ASN CYS ALA GLN ASN SEQRES 2 A 341 PRO ASN CYS ASN ILE MET ILE PHE HIS PRO THR LYS GLU SEQRES 3 A 341 GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA TYR MET GLU SEQRES 4 A 341 SER GLN GLY ALA HIS ARG ALA GLY LEU ALA LYS ILE ILE SEQRES 5 A 341 PRO PRO LYS GLU TRP LYS ALA ARG GLU THR TYR ASP ASN SEQRES 6 A 341 ILE SER GLU ILE LEU ILE ALA THR PRO LEU GLN GLN VAL SEQRES 7 A 341 ALA SER GLY ARG ALA GLY VAL PHE THR GLN TYR HIS LYS SEQRES 8 A 341 LYS LYS LYS ALA MET THR VAL GLY GLU TYR ARG HIS LEU SEQRES 9 A 341 ALA ASN SER LYS LYS TYR GLN THR PRO PRO HIS GLN ASN SEQRES 10 A 341 PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS ASN ARG ILE SEQRES 11 A 341 TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SER GLY SER SEQRES 12 A 341 LEU PHE ASP GLU ASN THR LYS GLN TRP ASN LEU GLY HIS SEQRES 13 A 341 LEU GLY THR ILE GLN ASP LEU LEU GLU LYS GLU CYS GLY SEQRES 14 A 341 VAL VAL ILE GLU GLY VAL ASN THR PRO TYR LEU TYR PHE SEQRES 15 A 341 GLY MET TRP LYS THR THR PHE ALA TRP HIS THR GLU ASP SEQRES 16 A 341 MET ASP LEU TYR SER ILE ASN TYR LEU HIS LEU GLY GLU SEQRES 17 A 341 PRO LYS THR TRP TYR VAL VAL PRO PRO GLU HIS GLY GLN SEQRES 18 A 341 ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE PRO GLY SER SEQRES 19 A 341 SER ARG GLY CYS GLY ALA PHE LEU ARG HIS LYS VAL ALA SEQRES 20 A 341 LEU ILE SER PRO THR VAL LEU LYS GLU ASN GLY ILE PRO SEQRES 21 A 341 PHE ASN ARG ILE THR GLN GLU ALA GLY GLU PHE MET VAL SEQRES 22 A 341 THR PHE PRO TYR GLY TYR HIS ALA GLY PHE ASN HIS GLY SEQRES 23 A 341 PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA THR PRO ARG SEQRES 24 A 341 TRP ILE ASP TYR GLY LYS MET ALA SER GLN CYS SER CYS SEQRES 25 A 341 GLY GLU ALA ARG VAL THR PHE SER MET ASP ALA PHE VAL SEQRES 26 A 341 ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU TRP LYS ARG SEQRES 27 A 341 GLY GLN ASP HET ZN A 401 1 HET NI 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 10 HET EDO A 410 10 HET EDO A 411 10 HET EDO A 412 10 HET SO4 A 413 5 HET SO4 A 414 5 HET SO4 A 415 5 HET I1L A 416 17 HET CL A 417 1 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM I1L [2-(2~{H}-1,2,3,4-TETRAZOL-5-YL)ETHANOYLAMINO]AZANIUM HETNAM CL CHLORIDE ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI NI 2+ FORMUL 4 NA NA 1+ FORMUL 5 EDO 9(C2 H6 O2) FORMUL 14 SO4 3(O4 S 2-) FORMUL 17 I1L C3 H7 N6 O 1+ FORMUL 18 CL CL 1- FORMUL 19 HOH *459(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 SER A 107 1 10 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 SER A 320 GLN A 329 1 10 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 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 ILE A 264 N TRP A 212 LINK OD1 ASN A 17 NA NA A 403 1555 8554 2.23 LINK NE2 HIS A 192 NI NI A 402 1555 1555 2.07 LINK OE2 GLU A 194 NI NI A 402 1555 1555 2.02 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.28 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.09 LINK NE2 HIS A 280 NI NI A 402 1555 1555 2.09 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.26 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.30 LINK NI NI A 402 OAIAI1L A 416 1555 1555 2.05 LINK NI NI A 402 NAJAI1L A 416 1555 1555 2.10 LINK NI NI A 402 O HOH A 738 1555 1555 2.14 LINK NA NA A 403 O HOH A 630 1555 8554 2.23 LINK NA NA A 403 O HOH A 649 1555 1555 2.40 LINK NA NA A 403 O HOH A 829 1555 1555 2.28 LINK NA NA A 403 O HOH A 829 1555 8554 2.28 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 5 HIS A 192 GLU A 194 HIS A 280 I1L A 416 SITE 2 AC2 5 HOH A 738 SITE 1 AC3 5 ASN A 17 ASN A 262 HOH A 630 HOH A 649 SITE 2 AC3 5 HOH A 829 SITE 1 AC4 5 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 2 AC4 5 HOH A 726 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 657 HOH A 680 SITE 1 AC6 4 THR A 252 LYS A 255 ARG A 263 EDO A 409 SITE 1 AC7 5 PHE A 118 GLU A 122 ARG A 263 THR A 265 SITE 2 AC7 5 HOH A 629 SITE 1 AC8 7 LYS A 109 GLN A 111 PRO A 113 ASN A 132 SITE 2 AC8 7 TRP A 185 LYS A 186 HOH A 514 SITE 1 AC9 7 GLU A 122 ARG A 123 TRP A 126 EDO A 406 SITE 2 AC9 7 HOH A 572 HOH A 603 HOH A 623 SITE 1 AD1 9 TYR A 179 TYR A 181 GLU A 194 SER A 200 SITE 2 AD1 9 ALA A 292 ASN A 294 I1L A 416 HOH A 738 SITE 3 AD1 9 HOH A 808 SITE 1 AD2 6 PHE A 31 ASP A 32 GLY A 158 PHE A 295 SITE 2 AD2 6 ALA A 296 HOH A 507 SITE 1 AD3 4 GLU A 27 TYR A 37 HOH A 521 HOH A 864 SITE 1 AD4 7 ARG A 60 THR A 62 ASP A 64 ASN A 65 SITE 2 AD4 7 HOH A 578 HOH A 597 HOH A 801 SITE 1 AD5 12 MET A 19 ILE A 20 LYS A 255 HOH A 541 SITE 2 AD5 12 HOH A 665 HOH A 770 HOH A 799 HOH A 812 SITE 3 AD5 12 HOH A 856 HOH A 894 HOH A 919 HOH A 935 SITE 1 AD6 6 ARG A 102 HIS A 103 ASN A 106 HOH A 504 SITE 2 AD6 6 HOH A 513 HOH A 565 SITE 1 AD7 15 TYR A 136 PHE A 189 HIS A 192 GLU A 194 SITE 2 AD7 15 SER A 200 ASN A 202 LYS A 210 TRP A 212 SITE 3 AD7 15 HIS A 280 NI A 402 EDO A 410 HOH A 538 SITE 4 AD7 15 HOH A 642 HOH A 738 HOH A 817 SITE 1 AD8 2 ASN A 128 LYS A 186 CRYST1 71.631 71.631 150.770 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 0.013960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006633 0.00000