HEADER OXIDOREDUCTASE/INHIBITOR 10-JUN-18 6DQ9 TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE COVALENT INHIBITOR N69 I.E. [2- TITLE 2 ((3-ACRYLAMIDOPHENYL)(2-(PIPERIDIN-1-YL)ETHOXY)METHYL)THIENO[3,2- TITLE 3 B]PYRIDINE-7-CARBOXYLIC 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 4 11-OCT-23 6DQ9 1 LINK REVDAT 3 01-JAN-20 6DQ9 1 REMARK REVDAT 2 01-MAY-19 6DQ9 1 JRNL REVDAT 1 21-NOV-18 6DQ9 0 JRNL AUTH J.R.HORTON,C.B.WOODCOCK,Q.CHEN,X.LIU,X.ZHANG,J.SHANKS,G.RAI, JRNL AUTH 2 B.T.MOTT,D.J.JANSEN,S.C.KALES,M.J.HENDERSON,M.CYR,K.POHIDA, JRNL AUTH 3 X.HU,P.SHAH,X.XU,A.JADHAV,D.J.MALONEY,M.D.HALL,A.SIMEONOV, JRNL AUTH 4 H.FU,P.M.VERTINO,X.CHENG JRNL TITL STRUCTURE-BASED ENGINEERING OF IRREVERSIBLE INHIBITORS JRNL TITL 2 AGAINST HISTONE LYSINE DEMETHYLASE KDM5A. JRNL REF J. MED. CHEM. V. 61 10588 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30392349 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01219 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. 1.75 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34011 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 1669 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 33.1060 - 3.9986 1.00 2744 179 0.1539 0.1645 REMARK 3 2 3.9986 - 3.1747 1.00 2693 161 0.1510 0.1903 REMARK 3 3 3.1747 - 2.7736 1.00 2766 69 0.1657 0.2046 REMARK 3 4 2.7736 - 2.5201 1.00 2723 147 0.1829 0.2254 REMARK 3 5 2.5201 - 2.3395 1.00 2661 149 0.1817 0.2168 REMARK 3 6 2.3395 - 2.2016 1.00 2722 128 0.1761 0.2059 REMARK 3 7 2.2016 - 2.0914 1.00 2691 140 0.1778 0.1914 REMARK 3 8 2.0914 - 2.0004 1.00 2655 156 0.1765 0.1865 REMARK 3 9 2.0004 - 1.9234 1.00 2732 130 0.1955 0.2248 REMARK 3 10 1.9234 - 1.8570 1.00 2663 130 0.2186 0.2763 REMARK 3 11 1.8570 - 1.7989 1.00 2675 129 0.2377 0.2623 REMARK 3 12 1.7989 - 1.7475 0.97 2617 151 0.2560 0.2544 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.170 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 : 0.002 2522 REMARK 3 ANGLE : 0.525 3448 REMARK 3 CHIRALITY : 0.043 356 REMARK 3 PLANARITY : 0.004 449 REMARK 3 DIHEDRAL : 3.769 1983 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9891 1.6593 9.2239 REMARK 3 T TENSOR REMARK 3 T11: 0.1516 T22: 0.1421 REMARK 3 T33: 0.1887 T12: 0.0260 REMARK 3 T13: -0.0086 T23: -0.0077 REMARK 3 L TENSOR REMARK 3 L11: 0.0196 L22: 0.0408 REMARK 3 L33: 0.0773 L12: 0.0278 REMARK 3 L13: 0.0717 L23: 0.0695 REMARK 3 S TENSOR REMARK 3 S11: 0.0292 S12: 0.0134 S13: 0.0428 REMARK 3 S21: 0.1445 S22: 0.0595 S23: -0.0259 REMARK 3 S31: 0.1853 S32: 0.0268 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 81 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.3494 13.4645 8.1195 REMARK 3 T TENSOR REMARK 3 T11: 0.1335 T22: 0.1554 REMARK 3 T33: 0.1843 T12: -0.0160 REMARK 3 T13: -0.0193 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 0.1083 L22: 0.1075 REMARK 3 L33: 0.1912 L12: 0.0473 REMARK 3 L13: -0.1240 L23: -0.0843 REMARK 3 S TENSOR REMARK 3 S11: -0.0338 S12: 0.0359 S13: 0.0071 REMARK 3 S21: 0.0049 S22: 0.0181 S23: -0.0354 REMARK 3 S31: -0.0508 S32: 0.0417 S33: -0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 82 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.7112 27.5344 20.5180 REMARK 3 T TENSOR REMARK 3 T11: 0.1856 T22: 0.1042 REMARK 3 T33: 0.1327 T12: 0.0074 REMARK 3 T13: -0.0127 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.0182 L22: 0.0383 REMARK 3 L33: 0.0214 L12: -0.0053 REMARK 3 L13: -0.0225 L23: 0.0090 REMARK 3 S TENSOR REMARK 3 S11: -0.0535 S12: -0.1171 S13: 0.1442 REMARK 3 S21: 0.0994 S22: 0.0489 S23: 0.0590 REMARK 3 S31: -0.1136 S32: -0.0436 S33: 0.0043 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 379 THROUGH 399 ) REMARK 3 ORIGIN FOR THE GROUP (A): -33.0482 12.6702 22.3812 REMARK 3 T TENSOR REMARK 3 T11: 0.1718 T22: 0.1425 REMARK 3 T33: 0.0962 T12: -0.0152 REMARK 3 T13: 0.0264 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.0209 L22: 0.0263 REMARK 3 L33: 0.0188 L12: -0.0158 REMARK 3 L13: 0.0065 L23: 0.0041 REMARK 3 S TENSOR REMARK 3 S11: -0.0929 S12: 0.0186 S13: -0.0186 REMARK 3 S21: 0.1714 S22: -0.0201 S23: 0.0413 REMARK 3 S31: 0.1824 S32: -0.1770 S33: -0.0117 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 400 THROUGH 432 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7487 24.8103 11.5071 REMARK 3 T TENSOR REMARK 3 T11: 0.1094 T22: 0.1099 REMARK 3 T33: 0.1906 T12: -0.0779 REMARK 3 T13: 0.0448 T23: -0.0398 REMARK 3 L TENSOR REMARK 3 L11: 0.0120 L22: 0.0750 REMARK 3 L33: 0.0835 L12: -0.0369 REMARK 3 L13: 0.0227 L23: 0.0651 REMARK 3 S TENSOR REMARK 3 S11: 0.0149 S12: 0.0234 S13: 0.0191 REMARK 3 S21: -0.0240 S22: 0.0729 S23: -0.0219 REMARK 3 S31: -0.3236 S32: -0.0407 S33: 0.0198 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.4983 16.3269 1.0029 REMARK 3 T TENSOR REMARK 3 T11: -0.1546 T22: 0.3414 REMARK 3 T33: 0.2207 T12: -0.0482 REMARK 3 T13: 0.0929 T23: -0.0441 REMARK 3 L TENSOR REMARK 3 L11: 0.0342 L22: 0.0360 REMARK 3 L33: 0.0198 L12: 0.0203 REMARK 3 L13: -0.0693 L23: -0.0220 REMARK 3 S TENSOR REMARK 3 S11: 0.1892 S12: 0.0474 S13: -0.0643 REMARK 3 S21: -0.4822 S22: 0.1415 S23: 0.0114 REMARK 3 S31: -0.2613 S32: 0.1575 S33: 0.0111 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0013 15.5836 6.5390 REMARK 3 T TENSOR REMARK 3 T11: 0.1326 T22: 0.1331 REMARK 3 T33: 0.1103 T12: -0.0217 REMARK 3 T13: -0.0052 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.0445 L22: 0.0734 REMARK 3 L33: 0.0510 L12: -0.0067 REMARK 3 L13: -0.0223 L23: 0.0132 REMARK 3 S TENSOR REMARK 3 S11: -0.0317 S12: 0.0077 S13: 0.0523 REMARK 3 S21: 0.0089 S22: 0.0249 S23: -0.0093 REMARK 3 S31: 0.0128 S32: 0.0030 S33: -0.0000 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.5158 9.4354 -5.1360 REMARK 3 T TENSOR REMARK 3 T11: 0.1808 T22: 0.1996 REMARK 3 T33: 0.1916 T12: -0.0340 REMARK 3 T13: -0.0337 T23: -0.0145 REMARK 3 L TENSOR REMARK 3 L11: 0.0047 L22: 0.0065 REMARK 3 L33: 0.0039 L12: 0.0010 REMARK 3 L13: -0.0032 L23: -0.0052 REMARK 3 S TENSOR REMARK 3 S11: -0.0316 S12: 0.1421 S13: 0.0784 REMARK 3 S21: -0.0508 S22: 0.0780 S23: 0.0292 REMARK 3 S31: 0.0480 S32: -0.0431 S33: 0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 547 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.8730 16.8056 0.0297 REMARK 3 T TENSOR REMARK 3 T11: 0.2429 T22: 0.1881 REMARK 3 T33: 0.2371 T12: -0.0030 REMARK 3 T13: 0.0394 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: -0.0082 L22: 0.0107 REMARK 3 L33: -0.0269 L12: -0.0081 REMARK 3 L13: -0.0041 L23: -0.0140 REMARK 3 S TENSOR REMARK 3 S11: 0.0694 S12: -0.0650 S13: -0.0409 REMARK 3 S21: -0.0489 S22: -0.0783 S23: -0.0682 REMARK 3 S31: -0.1103 S32: -0.1523 S33: -0.0000 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 548 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.9309 11.0245 6.1343 REMARK 3 T TENSOR REMARK 3 T11: 0.1366 T22: 0.1350 REMARK 3 T33: 0.1181 T12: -0.0257 REMARK 3 T13: 0.0001 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 0.0458 L22: 0.1075 REMARK 3 L33: 0.0522 L12: -0.0313 REMARK 3 L13: -0.0322 L23: -0.0385 REMARK 3 S TENSOR REMARK 3 S11: -0.0298 S12: 0.0340 S13: -0.0089 REMARK 3 S21: -0.0109 S22: 0.0509 S23: -0.0305 REMARK 3 S31: 0.0300 S32: 0.0167 S33: -0.0001 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 6DQ9 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_1000234893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-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-BM 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 MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34013 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.748 REMARK 200 RESOLUTION RANGE LOW (A) : 33.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.79400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 45.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 58.75850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.00050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.75850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.00050 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: 1310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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 886 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 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 THR A 344 REMARK 465 ARG A 345 REMARK 465 VAL A 346 REMARK 465 ARG A 347 REMARK 465 PRO A 348 REMARK 465 ARG A 349 REMARK 465 GLU A 350 REMARK 465 ALA A 351 REMARK 465 PHE A 352 REMARK 465 ALA A 457 REMARK 465 HIS A 458 REMARK 465 ILE A 459 REMARK 465 ASN A 460 REMARK 465 VAL A 461 REMARK 465 ASP A 462 REMARK 465 ILE A 463 REMARK 465 SER A 464 REMARK 465 GLY A 465 REMARK 465 MET A 466 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 LYS A 55 CG CD CE NZ REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 ARG A 69 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 364 CD OE1 NE2 REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 GLU A 402 CG CD OE1 OE2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 LYS A 425 CD CE NZ REMARK 470 ARG A 428 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 429 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 GLU A 434 CG CD OE1 OE2 REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 LEU A 456 CG CD1 CD2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 GLU A 520 CG CD OE1 OE2 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 477 -8.80 81.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 INHIBITOR N69 (PDB CHEMICAL COMPONENT H74) MAKES A COVALENT BOND TO REMARK 600 C481 OF KDM5A. THERE IS AN APPARENT LOSS OF A CARBON BEFORE THE REMARK 600 BOND IS FORMED. 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 91.0 REMARK 620 3 HIS A 571 NE2 85.3 88.8 REMARK 620 4 H74 A 601 N31 91.2 169.5 101.7 REMARK 620 5 HOH A 719 O 95.1 79.8 168.6 89.7 REMARK 620 6 HOH A 830 O 178.3 90.7 94.8 87.1 85.2 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 H74 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 GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 607 DBREF 6DQ9 A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6DQ9 A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6DQ9 HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6DQ9 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 H74 A 601 32 HET MN A 602 1 HET GOL A 603 6 HET DMS A 604 4 HET DMS A 605 4 HET EDO A 606 4 HET EDO A 607 4 HETNAM H74 2-{(R)-[3-(ACRYLOYLAMINO)PHENYL][2-(PIPERIDIN-1-YL) HETNAM 2 H74 ETHOXY]METHYL}THIENO[3,2-B]PYRIDINE-7-CARBOXYLIC ACID HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 H74 C25 H27 N3 O4 S FORMUL 3 MN MN 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 DMS 2(C2 H6 O S) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 9 HOH *209(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 GLU A 434 5 3 HELIX 7 AA7 GLU A 435 LEU A 440 1 6 HELIX 8 AA8 ASN A 444 MET A 448 5 5 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 530 GLN A 535 1 6 HELIX 13 AB4 LEU A 536 THR A 538 5 3 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 TRP A 470 O ALA A 583 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 GLN A 557 N LYS A 501 LINK SG CYS A 481 C17 H74 A 601 1555 1555 1.80 LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.19 LINK OE1 GLU A 485 MN MN A 602 1555 1555 2.14 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.24 LINK N31 H74 A 601 MN MN A 602 1555 1555 2.33 LINK MN MN A 602 O HOH A 719 1555 1555 2.24 LINK MN MN A 602 O HOH A 830 1555 1555 2.07 SITE 1 AC1 15 TYR A 409 ASP A 412 TYR A 472 PHE A 480 SITE 2 AC1 15 CYS A 481 HIS A 483 LYS A 501 TRP A 503 SITE 3 AC1 15 LEU A 536 HIS A 571 MN A 602 HOH A 750 SITE 4 AC1 15 HOH A 788 HOH A 806 HOH A 830 SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 H74 A 601 SITE 2 AC2 6 HOH A 719 HOH A 830 SITE 1 AC3 10 MET A 380 PRO A 381 GLU A 485 ASP A 486 SITE 2 AC3 10 HIS A 487 TRP A 488 LEU A 532 HOH A 702 SITE 3 AC3 10 HOH A 724 HOH A 843 SITE 1 AC4 8 ARG A 76 LEU A 77 GLU A 79 SER A 479 SITE 2 AC4 8 CYS A 481 ILE A 539 HOH A 742 HOH A 880 SITE 1 AC5 4 ARG A 519 ASP A 531 HIS A 534 GLN A 535 SITE 1 AC6 4 GLU A 12 ARG A 359 GLU A 360 TYR A 361 SITE 1 AC7 6 TRP A 395 PHE A 480 TRP A 482 ILE A 539 SITE 2 AC7 6 MET A 540 SER A 572 CRYST1 117.517 62.001 46.725 90.00 92.13 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 0.008509 0.000000 0.000317 0.00000 SCALE2 0.000000 0.016129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021417 0.00000