HEADER OXIDOREDUCTASE 02-DEC-17 6F5R TITLE CRYSTAL STRUCTURE OF KDM4D WITH GF028 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 6F5R 1 LINK REVDAT 1 12-DEC-18 6F5R 0 JRNL AUTH P.H.MALECKI,A.LINK,M.S.WEISS,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF KDM4D WITH GF028 LIGAND JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.61 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.890 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 99820 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2094 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.4172 - 3.9604 1.00 6508 138 0.1651 0.2046 REMARK 3 2 3.9604 - 3.1447 0.99 6509 134 0.1440 0.1477 REMARK 3 3 3.1447 - 2.7475 1.00 6517 144 0.1465 0.1478 REMARK 3 4 2.7475 - 2.4964 1.00 6520 143 0.1446 0.1760 REMARK 3 5 2.4964 - 2.3176 1.00 6525 144 0.1415 0.2045 REMARK 3 6 2.3176 - 2.1810 1.00 6535 139 0.1417 0.1651 REMARK 3 7 2.1810 - 2.0718 1.00 6543 134 0.1460 0.1884 REMARK 3 8 2.0718 - 1.9816 1.00 6530 143 0.1634 0.2110 REMARK 3 9 1.9816 - 1.9053 1.00 6514 142 0.1880 0.2081 REMARK 3 10 1.9053 - 1.8396 1.00 6527 139 0.2289 0.2960 REMARK 3 11 1.8396 - 1.7821 1.00 6536 140 0.2525 0.2314 REMARK 3 12 1.7821 - 1.7312 1.00 6505 143 0.2718 0.2659 REMARK 3 13 1.7312 - 1.6856 1.00 6558 138 0.2978 0.3555 REMARK 3 14 1.6856 - 1.6445 1.00 6503 141 0.3454 0.3351 REMARK 3 15 1.6445 - 1.6071 0.98 6396 132 0.3941 0.4225 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.37 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 : 0.012 2894 REMARK 3 ANGLE : 1.106 3924 REMARK 3 CHIRALITY : 0.066 388 REMARK 3 PLANARITY : 0.007 511 REMARK 3 DIHEDRAL : 14.618 1075 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 82 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.3512 -1.6298 -18.5173 REMARK 3 T TENSOR REMARK 3 T11: 0.1489 T22: 0.2088 REMARK 3 T33: 0.1883 T12: 0.0021 REMARK 3 T13: 0.0365 T23: -0.0116 REMARK 3 L TENSOR REMARK 3 L11: 0.7227 L22: 2.1205 REMARK 3 L33: 1.5094 L12: 0.4071 REMARK 3 L13: 0.0137 L23: -0.4321 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: 0.0002 S13: 0.0196 REMARK 3 S21: 0.0987 S22: -0.0331 S23: -0.2041 REMARK 3 S31: -0.1707 S32: 0.2070 S33: 0.0527 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 83 THROUGH 131 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.3233 -23.5525 -23.4876 REMARK 3 T TENSOR REMARK 3 T11: 0.1688 T22: 0.1453 REMARK 3 T33: 0.2036 T12: -0.0064 REMARK 3 T13: 0.0149 T23: -0.0298 REMARK 3 L TENSOR REMARK 3 L11: 1.8523 L22: 1.9897 REMARK 3 L33: 3.6524 L12: -0.8201 REMARK 3 L13: 1.4391 L23: -0.3994 REMARK 3 S TENSOR REMARK 3 S11: 0.0347 S12: 0.1321 S13: -0.1540 REMARK 3 S21: -0.0860 S22: -0.0420 S23: -0.0138 REMARK 3 S31: 0.2454 S32: 0.0832 S33: 0.0041 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 132 THROUGH 194 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.9572 -5.1055 -10.3086 REMARK 3 T TENSOR REMARK 3 T11: 0.1784 T22: 0.1985 REMARK 3 T33: 0.1672 T12: -0.0103 REMARK 3 T13: 0.0085 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.7894 L22: 0.7100 REMARK 3 L33: 0.5970 L12: -0.6576 REMARK 3 L13: -0.1087 L23: 0.0900 REMARK 3 S TENSOR REMARK 3 S11: -0.0680 S12: -0.1127 S13: 0.0064 REMARK 3 S21: 0.1336 S22: 0.0289 S23: 0.0142 REMARK 3 S31: -0.0086 S32: 0.0355 S33: 0.0447 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 195 THROUGH 306 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.1165 -5.8484 -24.0898 REMARK 3 T TENSOR REMARK 3 T11: 0.1544 T22: 0.1499 REMARK 3 T33: 0.1543 T12: -0.0017 REMARK 3 T13: 0.0198 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 0.6235 L22: 0.8541 REMARK 3 L33: 1.3728 L12: 0.2612 REMARK 3 L13: 0.4497 L23: 0.3945 REMARK 3 S TENSOR REMARK 3 S11: -0.0071 S12: 0.0451 S13: 0.0269 REMARK 3 S21: -0.0165 S22: -0.0205 S23: 0.0924 REMARK 3 S31: -0.0398 S32: -0.0537 S33: 0.0317 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 307 THROUGH 337 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.0478 -2.2403 -9.6610 REMARK 3 T TENSOR REMARK 3 T11: 0.2778 T22: 0.2625 REMARK 3 T33: 0.2925 T12: -0.0333 REMARK 3 T13: 0.0321 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 1.4095 L22: 5.6757 REMARK 3 L33: 3.7669 L12: 1.3715 REMARK 3 L13: -0.0818 L23: 3.8570 REMARK 3 S TENSOR REMARK 3 S11: -0.1002 S12: -0.0421 S13: -0.3663 REMARK 3 S21: 0.3047 S22: 0.0517 S23: 0.1580 REMARK 3 S31: 0.6849 S32: -0.2569 S33: 0.0214 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 6F5R 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_1200007786. 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 : 14.2 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 PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99966 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.378 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 5.643 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.43 REMARK 200 R MERGE FOR SHELL (I) : 2.34500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.640 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 (%): 53.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 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 76.19600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.07450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 114.29400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.07450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.09800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.07450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 114.29400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.07450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.07450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.09800 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 76.19600 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: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 755 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 815 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 ASN A 176 94.33 -160.41 REMARK 500 LYS A 186 -5.70 76.67 REMARK 500 MET A 196 19.34 58.37 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 412 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE2 96.6 REMARK 620 3 HIS A 280 NE2 84.9 86.6 REMARK 620 4 CQZ A 415 NAD 89.1 168.8 103.7 REMARK 620 5 HOH A 504 O 91.9 84.6 170.2 85.5 REMARK 620 6 HOH A 618 O 175.3 87.5 93.1 87.3 90.8 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 112.1 REMARK 620 3 CYS A 310 SG 113.8 110.8 REMARK 620 4 CYS A 312 SG 114.3 99.7 105.1 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 NI 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 CQZ A 415 DBREF 6F5R A 11 337 UNP Q6B0I6 KDM4D_HUMAN 11 337 SEQRES 1 A 327 ALA GLN ASN PRO ASN CYS ASN ILE MET ILE PHE HIS PRO SEQRES 2 A 327 THR LYS GLU GLU PHE ASN ASP PHE ASP LYS TYR ILE ALA SEQRES 3 A 327 TYR MET GLU SER GLN GLY ALA HIS ARG ALA GLY LEU ALA SEQRES 4 A 327 LYS ILE ILE PRO PRO LYS GLU TRP LYS ALA ARG GLU THR SEQRES 5 A 327 TYR ASP ASN ILE SER GLU ILE LEU ILE ALA THR PRO LEU SEQRES 6 A 327 GLN GLN VAL ALA SER GLY ARG ALA GLY VAL PHE THR GLN SEQRES 7 A 327 TYR HIS LYS LYS LYS LYS ALA MET THR VAL GLY GLU TYR SEQRES 8 A 327 ARG HIS LEU ALA ASN SER LYS LYS TYR GLN THR PRO PRO SEQRES 9 A 327 HIS GLN ASN PHE GLU ASP LEU GLU ARG LYS TYR TRP LYS SEQRES 10 A 327 ASN ARG ILE TYR ASN SER PRO ILE TYR GLY ALA ASP ILE SEQRES 11 A 327 SER GLY SER LEU PHE ASP GLU ASN THR LYS GLN TRP ASN SEQRES 12 A 327 LEU GLY HIS LEU GLY THR ILE GLN ASP LEU LEU GLU LYS SEQRES 13 A 327 GLU CYS GLY VAL VAL ILE GLU GLY VAL ASN THR PRO TYR SEQRES 14 A 327 LEU TYR PHE GLY MET TRP LYS THR THR PHE ALA TRP HIS SEQRES 15 A 327 THR GLU ASP MET ASP LEU TYR SER ILE ASN TYR LEU HIS SEQRES 16 A 327 LEU GLY GLU PRO LYS THR TRP TYR VAL VAL PRO PRO GLU SEQRES 17 A 327 HIS GLY GLN ARG LEU GLU ARG LEU ALA ARG GLU LEU PHE SEQRES 18 A 327 PRO GLY SER SER ARG GLY CYS GLY ALA PHE LEU ARG HIS SEQRES 19 A 327 LYS VAL ALA LEU ILE SER PRO THR VAL LEU LYS GLU ASN SEQRES 20 A 327 GLY ILE PRO PHE ASN ARG ILE THR GLN GLU ALA GLY GLU SEQRES 21 A 327 PHE MET VAL THR PHE PRO TYR GLY TYR HIS ALA GLY PHE SEQRES 22 A 327 ASN HIS GLY PHE ASN CYS ALA GLU ALA ILE ASN PHE ALA SEQRES 23 A 327 THR PRO ARG TRP ILE ASP TYR GLY LYS MET ALA SER GLN SEQRES 24 A 327 CYS SER CYS GLY GLU ALA ARG VAL THR PHE SER MET ASP SEQRES 25 A 327 ALA PHE VAL ARG ILE LEU GLN PRO GLU ARG TYR ASP LEU SEQRES 26 A 327 TRP LYS 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 NI A 412 1 HET SO4 A 413 5 HET SO4 A 414 5 HET CQZ A 415 14 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM NI NICKEL (II) ION HETNAM SO4 SULFATE ION HETNAM CQZ 2-(3-OXIDANYLPROPYLAMINO)PYRIDINE-4-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 NI NI 2+ FORMUL 14 SO4 2(O4 S 2-) FORMUL 16 CQZ C9 H12 N2 O3 FORMUL 17 HOH *326(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 ASN A 65 GLU A 68 5 4 HELIX 4 AA4 VAL A 98 ASN A 106 1 9 HELIX 5 AA5 ASN A 117 ARG A 129 1 13 HELIX 6 AA6 ILE A 130 ASN A 132 5 3 HELIX 7 AA7 THR A 159 GLY A 169 1 11 HELIX 8 AA8 GLU A 194 LEU A 198 5 5 HELIX 9 AA9 PRO A 216 GLU A 218 5 3 HELIX 10 AB1 HIS A 219 PHE A 231 1 13 HELIX 11 AB2 PHE A 231 CYS A 238 1 8 HELIX 12 AB3 ALA A 240 LYS A 245 5 6 HELIX 13 AB4 SER A 250 ASN A 257 1 8 HELIX 14 AB5 ARG A 299 ALA A 307 1 9 HELIX 15 AB6 THR A 318 GLN A 329 1 12 HELIX 16 AB7 GLN A 329 LYS A 337 1 9 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 HIS A 280 ASN A 284 -1 O GLY A 282 N PHE A 189 SHEET 3 AA3 4 LYS A 210 VAL A 214 -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 412 1555 1555 2.23 LINK OE2 GLU A 194 NI NI A 412 1555 1555 2.15 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.22 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.19 LINK NE2 HIS A 280 NI NI A 412 1555 1555 2.22 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.36 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.33 LINK NI NI A 412 NAD CQZ A 415 1555 1555 2.28 LINK NI NI A 412 O HOH A 504 1555 1555 2.15 LINK NI NI A 412 O HOH A 618 1555 1555 2.10 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 2 ASN A 128 LYS A 186 SITE 1 AC3 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128 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 591 HOH A 709 SITE 1 AC5 4 THR A 252 LYS A 255 ARG A 263 HOH A 663 SITE 1 AC6 5 SER A 80 THR A 87 LYS A 305 HOH A 522 SITE 2 AC6 5 HOH A 674 SITE 1 AC7 5 PHE A 118 GLU A 122 ARG A 263 THR A 265 SITE 2 AC7 5 EDO A 411 SITE 1 AC8 3 ILE A 20 HOH A 603 HOH A 673 SITE 1 AC9 4 TYR A 181 ALA A 292 CQZ A 415 HOH A 504 SITE 1 AD1 2 GLU A 27 HOH A 550 SITE 1 AD2 4 ILE A 264 THR A 265 EDO A 407 HOH A 727 SITE 1 AD3 6 HIS A 192 GLU A 194 HIS A 280 CQZ A 415 SITE 2 AD3 6 HOH A 504 HOH A 618 SITE 1 AD4 5 ASP A 64 ASN A 65 ILE A 66 SER A 67 SITE 2 AD4 5 ARG A 102 SITE 1 AD5 5 ARG A 102 HIS A 103 ASN A 106 HOH A 502 SITE 2 AD5 5 HOH A 666 SITE 1 AD6 13 TYR A 136 PHE A 189 ALA A 190 HIS A 192 SITE 2 AD6 13 LYS A 210 LYS A 245 HIS A 280 EDO A 409 SITE 3 AD6 13 NI A 412 HOH A 504 HOH A 533 HOH A 618 SITE 4 AD6 13 HOH A 639 CRYST1 72.149 72.149 152.392 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 0.013860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006562 0.00000