HEADER OXIDOREDUCTASE 02-DEC-17 6F5Q TITLE CRYSTAL STRUCTURE OF KDM4D WITH GF026 LIGAND 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, KDM4, LIGAND BINDING, LIGAND OPTIMIZATION, DRUG DEVELOPMENT, KEYWDS 2 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 6F5Q 1 REMARK LINK REVDAT 1 12-DEC-18 6F5Q 0 JRNL AUTH P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF KDM4D WITH GF026 LIGAND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.43 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.870 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 142701 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.470 REMARK 3 FREE R VALUE TEST SET COUNT : 2095 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 48.5561 - 3.5173 1.00 9387 143 0.1427 0.1662 REMARK 3 2 3.5173 - 2.7919 1.00 9433 140 0.1277 0.1412 REMARK 3 3 2.7919 - 2.4390 1.00 9420 139 0.1171 0.1416 REMARK 3 4 2.4390 - 2.2160 1.00 9462 139 0.1194 0.1310 REMARK 3 5 2.2160 - 2.0571 1.00 9421 142 0.1155 0.1662 REMARK 3 6 2.0571 - 1.9359 1.00 9435 138 0.1185 0.1722 REMARK 3 7 1.9359 - 1.8389 1.00 9458 141 0.1198 0.1722 REMARK 3 8 1.8389 - 1.7589 1.00 9384 145 0.1199 0.1533 REMARK 3 9 1.7589 - 1.6911 1.00 9483 140 0.1701 0.2430 REMARK 3 10 1.6911 - 1.6328 1.00 9389 138 0.1737 0.2103 REMARK 3 11 1.6328 - 1.5817 1.00 9418 139 0.1857 0.2160 REMARK 3 12 1.5817 - 1.5365 1.00 9424 138 0.2121 0.2705 REMARK 3 13 1.5365 - 1.4961 1.00 9462 141 0.2621 0.2647 REMARK 3 14 1.4961 - 1.4596 1.00 9369 143 0.3299 0.3705 REMARK 3 15 1.4596 - 1.4264 0.92 8661 129 0.4570 0.4533 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.25 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 : 0.010 3064 REMARK 3 ANGLE : 1.138 4179 REMARK 3 CHIRALITY : 0.087 415 REMARK 3 PLANARITY : 0.007 553 REMARK 3 DIHEDRAL : 16.265 1185 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 6F5Q 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_1200007784. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-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 : 143054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 48.528 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.754 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 1.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.880 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 (%): 52.90 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 75.83300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.21850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.21850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.74950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.21850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.21850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.91650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.21850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.21850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.74950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.21850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.21850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.91650 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 75.83300 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: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 819 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 823 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: 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 LYS A 255 CD - CE - NZ ANGL. DEV. = 14.8 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 -8.27 77.81 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 414 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 97.7 REMARK 620 3 HIS A 280 NE2 85.8 87.3 REMARK 620 4 CTK A 415 NAF 91.8 167.8 101.0 REMARK 620 5 HOH A 552 O 93.2 84.3 171.3 87.7 REMARK 620 6 HOH A 638 O 174.2 85.3 89.5 85.9 92.0 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 107.8 REMARK 620 3 CYS A 310 SG 118.8 109.4 REMARK 620 4 CYS A 312 SG 112.3 99.8 107.2 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 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 SO4 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 NI A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CTK A 415 DBREF 6F5Q 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 EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET SO4 A 412 5 HET SO4 A 413 5 HET NI A 414 1 HET CTK A 415 17 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM NI NICKEL (II) ION HETNAM CTK 2-[2-(METHYLSULFONYLAMINO)ETHYLAMINO]PYRIDINE-4- HETNAM 2 CTK CARBOXYLIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 CL CL 1- FORMUL 4 EDO 9(C2 H6 O2) FORMUL 13 SO4 2(O4 S 2-) FORMUL 15 NI NI 2+ FORMUL 16 CTK C9 H13 N3 O4 S FORMUL 17 HOH *454(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 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 181 O ALA A 290 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 NE2 HIS A 192 NI NI A 414 1555 1555 2.16 LINK OE2 GLU A 194 NI NI A 414 1555 1555 2.10 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.28 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.13 LINK NE2 HIS A 280 NI NI A 414 1555 1555 2.21 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.26 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.31 LINK NI NI A 414 NAF CTK A 415 1555 1555 2.19 LINK NI NI A 414 O HOH A 552 1555 1555 2.12 LINK NI NI A 414 O HOH A 638 1555 1555 2.07 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 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 2 AC3 6 HOH A 710 HOH A 791 SITE 1 AC4 7 LYS A 150 GLN A 151 TRP A 152 ASN A 153 SITE 2 AC4 7 HIS A 156 HOH A 675 HOH A 717 SITE 1 AC5 5 PRO A 251 THR A 252 LYS A 255 ARG A 263 SITE 2 AC5 5 EDO A 407 SITE 1 AC6 6 LYS A 109 GLN A 111 ASN A 132 TRP A 185 SITE 2 AC6 6 LYS A 186 HOH A 668 SITE 1 AC7 7 GLU A 122 ARG A 123 TRP A 126 EDO A 405 SITE 2 AC7 7 HOH A 532 HOH A 599 HOH A 605 SITE 1 AC8 6 PHE A 118 GLU A 122 ARG A 263 THR A 265 SITE 2 AC8 6 HOH A 572 HOH A 735 SITE 1 AC9 5 GLU A 27 TYR A 37 HOH A 637 HOH A 640 SITE 2 AC9 5 HOH A 831 SITE 1 AD1 5 LYS A 25 GLU A 26 ASN A 106 HOH A 505 SITE 2 AD1 5 HOH A 715 SITE 1 AD2 5 TYR A 181 ILE A 293 ASN A 294 HOH A 520 SITE 2 AD2 5 HOH A 552 SITE 1 AD3 7 ARG A 60 THR A 62 ASN A 65 HOH A 513 SITE 2 AD3 7 HOH A 575 HOH A 771 HOH A 790 SITE 1 AD4 6 ARG A 102 HIS A 103 ASN A 106 HOH A 503 SITE 2 AD4 6 HOH A 536 HOH A 559 SITE 1 AD5 6 HIS A 192 GLU A 194 HIS A 280 CTK A 415 SITE 2 AD5 6 HOH A 552 HOH A 638 SITE 1 AD6 15 HIS A 90 TYR A 136 THR A 188 PHE A 189 SITE 2 AD6 15 ALA A 190 HIS A 192 ASN A 202 LYS A 210 SITE 3 AD6 15 HIS A 280 NI A 414 HOH A 552 HOH A 638 SITE 4 AD6 15 HOH A 708 HOH A 746 HOH A 787 CRYST1 72.437 72.437 151.666 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 0.013805 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013805 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006593 0.00000