HEADER OXIDOREDUCTASE/INHIBITOR 10-JUN-18 6DQC TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N50 I.E. 2-(4-((2- TITLE 2 (DIMETHYLAMINO)ETHYL)(ETHYL)CARBAMOYL)-5-(4-METHOXYPHENYL)-1H- TITLE 3 PYRAZOL-1-YL)ISONICOTINIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: LINKED KDM5A JMJ DOMAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 5 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2,HISTONE COMPND 6 DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1A, COMPND 7 RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2; COMPND 8 EC: 1.14.11.-; COMPND 9 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: KDM5A, JARID1A, RBBP2, RBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD C-PLUS KEYWDS DEMETHYLASE INHIBITION, OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 11-OCT-23 6DQC 1 REMARK REVDAT 2 01-JAN-20 6DQC 1 REMARK REVDAT 1 12-JUN-19 6DQC 0 JRNL AUTH J.R.HORTON,X.LIU,C.B.WOODCOCK,J.SHANKS,X.ZHANG,G.RAI,B.MOTT, JRNL AUTH 2 D.J.JANSEN,S.KALES,M.J.HENDERSON,K.POHIDA,Y.FANG,X.HU, JRNL AUTH 3 A.JADHAV,D.MALONEY,M.D.HALL,A.SIMEONOV,H.FU,P.M.VERTINO, JRNL AUTH 4 X.CHENG JRNL TITL TO BE DETERMINED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.HORTON,X.LIU,M.GALE,L.WU,J.R.SHANKS,X.ZHANG,P.J.WEBBER, REMARK 1 AUTH 2 J.S.BELL,S.C.KALES,B.T.MOTT,G.RAI,D.J.JANSEN,M.J.HENDERSON, REMARK 1 AUTH 3 D.J.URBAN,M.D.HALL,A.SIMEONOV,D.J.MALONEY,M.A.JOHNS,H.FU, REMARK 1 AUTH 4 A.JADHAV,P.M.VERTINO,Q.YAN,X.CHENG REMARK 1 TITL STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLASE REMARK 1 TITL 2 INHIBITION BY DIVERSE COMPOUNDS. REMARK 1 REF CELL CHEM BIOL V. 23 769 2016 REMARK 1 REFN ESSN 2451-9456 REMARK 1 PMID 27427228 REMARK 1 DOI 10.1016/J.CHEMBIOL.2016.06.006 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.R.HORTON,A.ENGSTROM,E.L.ZOELLER,X.LIU,J.R.SHANKS,X.ZHANG, REMARK 1 AUTH 2 M.A.JOHNS,P.M.VERTINO,H.FU,X.CHENG REMARK 1 TITL CHARACTERIZATION OF A LINKED JUMONJI DOMAIN OF THE REMARK 1 TITL 2 KDM5/JARID1 FAMILY OF HISTONE H3 LYSINE 4 DEMETHYLASES. REMARK 1 REF J. BIOL. CHEM. V. 291 2631 2016 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 26645689 REMARK 1 DOI 10.1074/JBC.M115.698449 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.R.HORTON,X.LIU,L.WU,K.ZHANG,J.SHANKS,X.ZHANG,G.RAI, REMARK 1 AUTH 2 B.T.MOTT,D.J.JANSEN,S.C.KALES,M.J.HENDERSON,K.POHIDA,Y.FANG, REMARK 1 AUTH 3 X.HU,A.JADHAV,D.J.MALONEY,M.D.HALL,A.SIMEONOV,H.FU, REMARK 1 AUTH 4 P.M.VERTINO,Q.YAN,X.CHENG REMARK 1 TITL INSIGHTS INTO THE ACTION OF INHIBITOR ENANTIOMERS AGAINST REMARK 1 TITL 2 HISTONE LYSINE DEMETHYLASE 5A. REMARK 1 REF J. MED. CHEM. V. 61 3193 2018 REMARK 1 REFN ISSN 1520-4804 REMARK 1 PMID 29537847 REMARK 1 DOI 10.1021/ACS.JMEDCHEM.8B00261 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 33465 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1701 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 35.8360 - 4.0154 1.00 2718 149 0.1813 0.1850 REMARK 3 2 4.0154 - 3.1878 1.00 2673 150 0.1829 0.2185 REMARK 3 3 3.1878 - 2.7850 1.00 2643 151 0.1942 0.2010 REMARK 3 4 2.7850 - 2.5305 1.00 2675 134 0.1963 0.2113 REMARK 3 5 2.5305 - 2.3491 1.00 2621 139 0.1950 0.2577 REMARK 3 6 2.3491 - 2.2106 1.00 2646 132 0.1850 0.2452 REMARK 3 7 2.2106 - 2.0999 1.00 2669 148 0.1875 0.2043 REMARK 3 8 2.0999 - 2.0085 1.00 2608 143 0.1895 0.2171 REMARK 3 9 2.0085 - 1.9312 1.00 2664 136 0.1911 0.2093 REMARK 3 10 1.9312 - 1.8646 1.00 2637 137 0.2115 0.2601 REMARK 3 11 1.8646 - 1.8063 1.00 2626 143 0.2202 0.2409 REMARK 3 12 1.8063 - 1.7550 0.97 2584 139 0.2359 0.2755 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 2605 REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : 0.050 364 REMARK 3 PLANARITY : 0.006 464 REMARK 3 DIHEDRAL : 3.501 2068 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): -19.2608 2.4671 9.2274 REMARK 3 T TENSOR REMARK 3 T11: 0.1673 T22: 0.1459 REMARK 3 T33: 0.1991 T12: 0.0138 REMARK 3 T13: -0.0242 T23: -0.0042 REMARK 3 L TENSOR REMARK 3 L11: 5.5873 L22: 2.6613 REMARK 3 L33: 2.0177 L12: -0.3782 REMARK 3 L13: 0.8019 L23: 0.4136 REMARK 3 S TENSOR REMARK 3 S11: 0.1056 S12: 0.3487 S13: -0.1378 REMARK 3 S21: 0.1210 S22: 0.0903 S23: -0.4355 REMARK 3 S31: 0.0920 S32: 0.2545 S33: -0.1853 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0294 5.5671 5.0855 REMARK 3 T TENSOR REMARK 3 T11: 0.1841 T22: 0.2209 REMARK 3 T33: 0.2605 T12: -0.0248 REMARK 3 T13: -0.0235 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 2.1316 L22: 2.5035 REMARK 3 L33: 1.5294 L12: 1.3582 REMARK 3 L13: 0.3954 L23: 1.1164 REMARK 3 S TENSOR REMARK 3 S11: -0.0746 S12: 0.0422 S13: -0.2908 REMARK 3 S21: 0.0056 S22: 0.1867 S23: -0.2632 REMARK 3 S31: -0.0568 S32: 0.2804 S33: -0.1274 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.6152 31.2040 12.5897 REMARK 3 T TENSOR REMARK 3 T11: 0.3516 T22: 0.2772 REMARK 3 T33: 0.2550 T12: 0.0196 REMARK 3 T13: -0.0184 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 2.2902 L22: 2.5190 REMARK 3 L33: 1.7435 L12: -1.5565 REMARK 3 L13: -0.7862 L23: -0.1525 REMARK 3 S TENSOR REMARK 3 S11: -0.1187 S12: -0.1293 S13: 0.7130 REMARK 3 S21: 0.0490 S22: 0.0865 S23: 0.1668 REMARK 3 S31: -0.4135 S32: -0.3256 S33: 0.0254 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.0712 19.8112 22.0920 REMARK 3 T TENSOR REMARK 3 T11: 0.2269 T22: 0.1680 REMARK 3 T33: 0.1717 T12: 0.0374 REMARK 3 T13: 0.0290 T23: -0.0127 REMARK 3 L TENSOR REMARK 3 L11: 1.3880 L22: 1.8864 REMARK 3 L33: 2.4954 L12: 0.6953 REMARK 3 L13: 0.1413 L23: 0.0020 REMARK 3 S TENSOR REMARK 3 S11: -0.0711 S12: -0.0757 S13: 0.0854 REMARK 3 S21: 0.1824 S22: 0.0135 S23: 0.1083 REMARK 3 S31: -0.0944 S32: -0.1909 S33: 0.0524 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 454 ) REMARK 3 ORIGIN FOR THE GROUP (A): -7.8834 21.4834 6.4037 REMARK 3 T TENSOR REMARK 3 T11: 0.2198 T22: 0.2721 REMARK 3 T33: 0.2412 T12: -0.0908 REMARK 3 T13: 0.0199 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 1.8560 L22: 1.0225 REMARK 3 L33: 0.4357 L12: -0.8355 REMARK 3 L13: -0.0454 L23: 0.3532 REMARK 3 S TENSOR REMARK 3 S11: 0.1787 S12: -0.1170 S13: 0.2004 REMARK 3 S21: -0.0664 S22: -0.0311 S23: -0.3005 REMARK 3 S31: -0.3101 S32: 0.3637 S33: -0.1088 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 455 THROUGH 485 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.0486 21.4857 0.4337 REMARK 3 T TENSOR REMARK 3 T11: 0.1725 T22: 0.1514 REMARK 3 T33: 0.1424 T12: -0.0223 REMARK 3 T13: 0.0287 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 0.7968 L22: 1.1275 REMARK 3 L33: 1.5072 L12: -0.3659 REMARK 3 L13: 0.4396 L23: 0.3613 REMARK 3 S TENSOR REMARK 3 S11: 0.0110 S12: 0.2219 S13: 0.0523 REMARK 3 S21: -0.2096 S22: -0.0618 S23: -0.1758 REMARK 3 S31: -0.2072 S32: 0.2304 S33: -0.0063 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 486 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.2624 13.5062 3.0136 REMARK 3 T TENSOR REMARK 3 T11: 0.1471 T22: 0.1255 REMARK 3 T33: 0.1440 T12: -0.0086 REMARK 3 T13: 0.0095 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.1106 L22: 1.2098 REMARK 3 L33: 1.6364 L12: 0.0796 REMARK 3 L13: 0.2251 L23: 0.2604 REMARK 3 S TENSOR REMARK 3 S11: -0.0033 S12: 0.0628 S13: -0.0285 REMARK 3 S21: -0.0807 S22: -0.0094 S23: 0.0936 REMARK 3 S31: -0.0090 S32: -0.0987 S33: 0.0075 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 6DQC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234897. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6-9.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33474 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.755 REMARK 200 RESOLUTION RANGE LOW (A) : 35.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5IVB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2-1.35 M (NH4)2SO4, 0.1 M TRIS-HCL REMARK 280 (PH 8.6-9.2) 0-20% GLYCEROL 25 MM (NA/K) DIBASIC/MONOBASIC REMARK 280 PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 58.56750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.01650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.56750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.01650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 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 HIS A -1 REMARK 465 ASN A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 GLY A 3 REMARK 465 VAL A 4 REMARK 465 GLY A 5 REMARK 465 PRO A 6 REMARK 465 GLY A 7 REMARK 465 GLY A 8 REMARK 465 TYR A 9 REMARK 465 ALA A 10 REMARK 465 ARG A 85 REMARK 465 VAL A 86 REMARK 465 ARG A 87 REMARK 465 ASP A 462 REMARK 465 ILE A 463 REMARK 465 SER A 464 REMARK 465 GLY A 465 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 THR A 30 OG1 CG2 REMARK 470 GLN A 58 CG CD OE1 NE2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 ARG A 349 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 350 CG CD OE1 OE2 REMARK 470 ASP A 376 CG OD1 OD2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 ARG A 428 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 431 CG1 CG2 CD1 REMARK 470 GLU A 434 CG CD OE1 OE2 REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 VAL A 461 CG1 CG2 REMARK 470 MET A 466 CG SD CE REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 ARG A 519 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 524 CG CD OE1 OE2 REMARK 470 GLU A 527 CG CD OE1 OE2 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 PHE A 29 32.50 -84.38 REMARK 500 PHE A 477 -5.21 80.07 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 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 483 NE2 REMARK 620 2 GLU A 485 OE1 93.8 REMARK 620 3 HIS A 571 NE2 85.9 91.6 REMARK 620 4 H5Y A 601 N17 89.4 166.4 101.8 REMARK 620 5 H5Y A 601 N25 83.9 95.9 167.7 71.2 REMARK 620 6 HOH A 750 O 171.6 94.6 93.4 82.5 95.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue H5Y A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 605 DBREF 6DQC A 1 87 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6DQC A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6DQC HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6DQC ASN A 0 UNP P29375 EXPRESSION TAG SEQRES 1 A 330 HIS ASN MET ALA GLY VAL GLY PRO GLY GLY TYR ALA ALA SEQRES 2 A 330 GLU PHE VAL PRO PRO PRO GLU CYS PRO VAL PHE GLU PRO SEQRES 3 A 330 SER TRP GLU GLU PHE THR ASP PRO LEU SER PHE ILE GLY SEQRES 4 A 330 ARG ILE ARG PRO LEU ALA GLU LYS THR GLY ILE CYS LYS SEQRES 5 A 330 ILE ARG PRO PRO LYS ASP TRP GLN PRO PRO PHE ALA CYS SEQRES 6 A 330 GLU VAL LYS SER PHE ARG PHE THR PRO ARG VAL GLN ARG SEQRES 7 A 330 LEU ASN GLU LEU GLU ALA MET THR ARG VAL ARG PRO ARG SEQRES 8 A 330 GLU ALA PHE GLY PHE GLU GLN ALA VAL ARG GLU TYR THR SEQRES 9 A 330 LEU GLN SER PHE GLY GLU MET ALA ASP ASN PHE LYS SER SEQRES 10 A 330 ASP TYR PHE ASN MET PRO VAL HIS MET VAL PRO THR GLU SEQRES 11 A 330 LEU VAL GLU LYS GLU PHE TRP ARG LEU VAL SER SER ILE SEQRES 12 A 330 GLU GLU ASP VAL ILE VAL GLU TYR GLY ALA ASP ILE SER SEQRES 13 A 330 SER LYS ASP PHE GLY SER GLY PHE PRO VAL LYS ASP GLY SEQRES 14 A 330 ARG ARG LYS ILE LEU PRO GLU GLU GLU GLU TYR ALA LEU SEQRES 15 A 330 SER GLY TRP ASN LEU ASN ASN MET PRO VAL LEU GLU GLN SEQRES 16 A 330 SER VAL LEU ALA HIS ILE ASN VAL ASP ILE SER GLY MET SEQRES 17 A 330 LYS VAL PRO TRP LEU TYR VAL GLY MET CYS PHE SER SER SEQRES 18 A 330 PHE CYS TRP HIS ILE GLU ASP HIS TRP SER TYR SER ILE SEQRES 19 A 330 ASN TYR LEU HIS TRP GLY GLU PRO LYS THR TRP TYR GLY SEQRES 20 A 330 VAL PRO SER HIS ALA ALA GLU GLN LEU GLU GLU VAL MET SEQRES 21 A 330 ARG GLU LEU ALA PRO GLU LEU PHE GLU SER GLN PRO ASP SEQRES 22 A 330 LEU LEU HIS GLN LEU VAL THR ILE MET ASN PRO ASN VAL SEQRES 23 A 330 LEU MET GLU HIS GLY VAL PRO VAL TYR ARG THR ASN GLN SEQRES 24 A 330 CYS ALA GLY GLU PHE VAL VAL THR PHE PRO ARG ALA TYR SEQRES 25 A 330 HIS SER GLY PHE ASN GLN GLY TYR ASN PHE ALA GLU ALA SEQRES 26 A 330 VAL ASN PHE CYS THR HET H5Y A 601 32 HET MN A 602 1 HET DMS A 603 4 HET GOL A 604 6 HET SO4 A 605 5 HETNAM H5Y 2-[4-{[2-(DIMETHYLAMINO)ETHYL](ETHYL)CARBAMOYL}-5-(4- HETNAM 2 H5Y METHOXYPHENYL)-1H-PYRAZOL-1-YL]PYRIDINE-4-CARBOXYLIC HETNAM 3 H5Y ACID HETNAM MN MANGANESE (II) ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 H5Y C23 H27 N5 O4 FORMUL 3 MN MN 2+ FORMUL 4 DMS C2 H6 O S FORMUL 5 GOL C3 H8 O3 FORMUL 6 SO4 O4 S 2- FORMUL 7 HOH *162(H2 O) HELIX 1 AA1 ASP A 31 GLU A 44 1 14 HELIX 2 AA2 LEU A 363 ASN A 379 1 17 HELIX 3 AA3 PRO A 381 VAL A 385 5 5 HELIX 4 AA4 PRO A 386 SER A 400 1 15 HELIX 5 AA5 SER A 415 GLY A 419 1 5 HELIX 6 AA6 LEU A 432 SER A 441 1 10 HELIX 7 AA7 ASN A 444 MET A 448 5 5 HELIX 8 AA8 VAL A 455 ASN A 460 1 6 HELIX 9 AA9 GLU A 485 SER A 489 5 5 HELIX 10 AB1 PRO A 507 HIS A 509 5 3 HELIX 11 AB2 ALA A 510 ALA A 522 1 13 HELIX 12 AB3 PRO A 523 SER A 528 1 6 HELIX 13 AB4 PRO A 530 GLN A 535 1 6 HELIX 14 AB5 ASN A 541 HIS A 548 1 8 SHEET 1 AA1 8 VAL A 21 PHE A 22 0 SHEET 2 AA1 8 ILE A 48 ILE A 51 1 O LYS A 50 N PHE A 22 SHEET 3 AA1 8 PHE A 562 THR A 565 -1 O PHE A 562 N ILE A 51 SHEET 4 AA1 8 TYR A 490 GLY A 498 -1 N SER A 491 O THR A 565 SHEET 5 AA1 8 ASN A 579 PHE A 586 -1 O GLU A 582 N TYR A 494 SHEET 6 AA1 8 TRP A 470 GLY A 474 -1 N TYR A 472 O ALA A 581 SHEET 7 AA1 8 ILE A 406 SER A 414 -1 N ILE A 413 O LEU A 471 SHEET 8 AA1 8 ARG A 73 ARG A 76 -1 N GLN A 75 O VAL A 407 SHEET 1 AA2 2 ARG A 69 PHE A 70 0 SHEET 2 AA2 2 TYR A 361 THR A 362 -1 O TYR A 361 N PHE A 70 SHEET 1 AA3 4 SER A 479 HIS A 483 0 SHEET 2 AA3 4 HIS A 571 ASN A 575 -1 O GLY A 573 N PHE A 480 SHEET 3 AA3 4 LYS A 501 GLY A 505 -1 N THR A 502 O PHE A 574 SHEET 4 AA3 4 TYR A 553 GLN A 557 -1 O THR A 555 N TRP A 503 LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.26 LINK OE1 GLU A 485 MN MN A 602 1555 1555 2.08 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.31 LINK N17 H5Y A 601 MN MN A 602 1555 1555 2.32 LINK N25 H5Y A 601 MN MN A 602 1555 1555 2.33 LINK MN MN A 602 O HOH A 750 1555 1555 2.20 SITE 1 AC1 18 ARG A 73 GLN A 75 TYR A 409 ALA A 411 SITE 2 AC1 18 TYR A 472 SER A 479 PHE A 480 HIS A 483 SITE 3 AC1 18 GLU A 485 ASP A 486 LYS A 501 TRP A 503 SITE 4 AC1 18 HIS A 571 MN A 602 DMS A 603 HOH A 750 SITE 5 AC1 18 HOH A 806 HOH A 812 SITE 1 AC2 5 HIS A 483 GLU A 485 HIS A 571 H5Y A 601 SITE 2 AC2 5 HOH A 750 SITE 1 AC3 5 TYR A 472 ALA A 583 ASN A 585 H5Y A 601 SITE 2 AC3 5 HOH A 748 SITE 1 AC4 4 ASN A 556 HOH A 702 HOH A 776 HOH A 818 SITE 1 AC5 4 GLU A 64 VAL A 65 LYS A 66 ARG A 429 CRYST1 117.135 62.033 46.661 90.00 92.21 90.00 C 1 2 1 4 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 0.008537 0.000000 0.000330 0.00000 SCALE2 0.000000 0.016120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021447 0.00000