HEADER OXIDOREDUCTASE/INHIBITOR 29-OCT-17 6BH1 TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (S)-2-((2- TITLE 2 CHLOROPHENYL)(2-(PIPERIDIN-1-YL)ETHOXY)METHYL)-1L2-PYRROLO[3,2- TITLE 3 B]PYRIDINE-7-CARBOXYLIC ACID (COMPOUND N52) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5A, 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; COMPND 6 EC: 1.14.11.-; COMPND 7 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-OXIDOREDUCTASE INHIBITOR KEYWDS 2 COMPLEX, OXIDOREDUCTASE, OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 4 04-OCT-23 6BH1 1 LINK REVDAT 3 01-JAN-20 6BH1 1 REMARK REVDAT 2 25-APR-18 6BH1 1 JRNL REVDAT 1 28-MAR-18 6BH1 0 JRNL AUTH J.R.HORTON,X.LIU,L.WU,K.ZHANG,J.SHANKS,X.ZHANG,G.RAI, JRNL AUTH 2 B.T.MOTT,D.J.JANSEN,S.C.KALES,M.J.HENDERSON,K.POHIDA,Y.FANG, JRNL AUTH 3 X.HU,A.JADHAV,D.J.MALONEY,M.D.HALL,A.SIMEONOV,H.FU, JRNL AUTH 4 P.M.VERTINO,Q.YAN,X.CHENG JRNL TITL INSIGHTS INTO THE ACTION OF INHIBITOR ENANTIOMERS AGAINST JRNL TITL 2 HISTONE LYSINE DEMETHYLASE 5A. JRNL REF J. MED. CHEM. V. 61 3193 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 29537847 JRNL DOI 10.1021/ACS.JMEDCHEM.8B00261 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 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 24382 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1218 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 27.2772 - 4.0149 1.00 2688 141 0.1510 0.1630 REMARK 3 2 4.0149 - 3.1883 1.00 2642 132 0.1439 0.1532 REMARK 3 3 3.1883 - 2.7858 1.00 2625 143 0.1547 0.1779 REMARK 3 4 2.7858 - 2.5313 1.00 2616 134 0.1681 0.2003 REMARK 3 5 2.5313 - 2.3499 1.00 2594 139 0.1697 0.2137 REMARK 3 6 2.3499 - 2.2115 1.00 2613 123 0.1660 0.2017 REMARK 3 7 2.2115 - 2.1007 1.00 2612 141 0.1731 0.2428 REMARK 3 8 2.1007 - 2.0093 1.00 2612 145 0.1786 0.2034 REMARK 3 9 2.0093 - 1.9320 0.85 2162 120 0.2150 0.2417 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.590 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 : 0.005 2453 REMARK 3 ANGLE : 0.724 3364 REMARK 3 CHIRALITY : 0.049 351 REMARK 3 PLANARITY : 0.006 438 REMARK 3 DIHEDRAL : 13.770 1420 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): -18.4974 2.6778 8.9097 REMARK 3 T TENSOR REMARK 3 T11: 0.1794 T22: 0.1665 REMARK 3 T33: 0.2629 T12: 0.0257 REMARK 3 T13: -0.0224 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 7.9563 L22: 3.8846 REMARK 3 L33: 3.3162 L12: -0.8587 REMARK 3 L13: 0.9993 L23: 0.4274 REMARK 3 S TENSOR REMARK 3 S11: -0.0664 S12: 0.0003 S13: -0.3438 REMARK 3 S21: 0.1286 S22: 0.2103 S23: -0.5442 REMARK 3 S31: 0.2536 S32: 0.5115 S33: -0.1027 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.7558 5.9020 4.8740 REMARK 3 T TENSOR REMARK 3 T11: 0.1421 T22: 0.2044 REMARK 3 T33: 0.2476 T12: -0.0099 REMARK 3 T13: -0.0108 T23: 0.0310 REMARK 3 L TENSOR REMARK 3 L11: 5.2904 L22: 5.4244 REMARK 3 L33: 3.1762 L12: 2.9924 REMARK 3 L13: 1.1926 L23: 2.8503 REMARK 3 S TENSOR REMARK 3 S11: -0.0863 S12: 0.1554 S13: -0.2660 REMARK 3 S21: -0.0560 S22: 0.2763 S23: -0.5004 REMARK 3 S31: -0.1042 S32: 0.5446 S33: -0.1638 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.6894 29.2269 12.8195 REMARK 3 T TENSOR REMARK 3 T11: 0.3847 T22: 0.1698 REMARK 3 T33: 0.2149 T12: 0.0731 REMARK 3 T13: -0.0391 T23: 0.0218 REMARK 3 L TENSOR REMARK 3 L11: 5.9816 L22: 6.4590 REMARK 3 L33: 4.4446 L12: 3.8056 REMARK 3 L13: 0.6653 L23: 1.3440 REMARK 3 S TENSOR REMARK 3 S11: -0.4880 S12: 0.2346 S13: 0.9335 REMARK 3 S21: -0.1549 S22: 0.1710 S23: 0.4049 REMARK 3 S31: -0.8010 S32: -0.1851 S33: 0.2735 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 399 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.2396 19.4593 22.8677 REMARK 3 T TENSOR REMARK 3 T11: 0.1999 T22: 0.1692 REMARK 3 T33: 0.1325 T12: 0.0407 REMARK 3 T13: 0.0392 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 2.8071 L22: 3.7698 REMARK 3 L33: 3.8734 L12: 1.7000 REMARK 3 L13: 0.6957 L23: 0.8523 REMARK 3 S TENSOR REMARK 3 S11: 0.0268 S12: -0.2446 S13: 0.0774 REMARK 3 S21: 0.4286 S22: -0.0983 S23: 0.1588 REMARK 3 S31: -0.0928 S32: -0.2500 S33: 0.0604 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 400 THROUGH 432 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3578 26.1110 11.2712 REMARK 3 T TENSOR REMARK 3 T11: 0.3409 T22: 0.1830 REMARK 3 T33: 0.2421 T12: -0.0841 REMARK 3 T13: 0.0066 T23: -0.0282 REMARK 3 L TENSOR REMARK 3 L11: 6.1920 L22: 2.8476 REMARK 3 L33: 2.8829 L12: -0.8572 REMARK 3 L13: -0.1656 L23: 0.2738 REMARK 3 S TENSOR REMARK 3 S11: 0.0898 S12: 0.1076 S13: 0.8039 REMARK 3 S21: -0.0039 S22: 0.1459 S23: -0.4043 REMARK 3 S31: -0.5400 S32: 0.4312 S33: -0.1748 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9561 17.4966 0.4681 REMARK 3 T TENSOR REMARK 3 T11: 0.2316 T22: 0.4074 REMARK 3 T33: 0.3200 T12: -0.0284 REMARK 3 T13: 0.0714 T23: -0.0349 REMARK 3 L TENSOR REMARK 3 L11: 4.5259 L22: 5.9837 REMARK 3 L33: 2.0262 L12: 0.1777 REMARK 3 L13: -1.5414 L23: 0.7379 REMARK 3 S TENSOR REMARK 3 S11: 0.3947 S12: 0.2816 S13: -0.2729 REMARK 3 S21: -0.5082 S22: -0.0030 S23: 0.0790 REMARK 3 S31: -0.2577 S32: 0.3774 S33: -0.3749 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.9245 16.5942 6.5697 REMARK 3 T TENSOR REMARK 3 T11: 0.1500 T22: 0.0967 REMARK 3 T33: 0.1091 T12: -0.0131 REMARK 3 T13: 0.0165 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 1.5174 L22: 1.8531 REMARK 3 L33: 2.6386 L12: 0.3119 REMARK 3 L13: 0.9040 L23: 1.1035 REMARK 3 S TENSOR REMARK 3 S11: -0.0123 S12: 0.0962 S13: 0.0009 REMARK 3 S21: -0.1346 S22: 0.0307 S23: -0.0469 REMARK 3 S31: -0.2008 S32: 0.1606 S33: -0.0144 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.4706 10.0826 -4.9988 REMARK 3 T TENSOR REMARK 3 T11: 0.2509 T22: 0.3325 REMARK 3 T33: 0.3010 T12: 0.0328 REMARK 3 T13: -0.0542 T23: -0.0324 REMARK 3 L TENSOR REMARK 3 L11: 5.2120 L22: 9.3837 REMARK 3 L33: 3.2971 L12: -6.6110 REMARK 3 L13: -4.0429 L23: 4.7203 REMARK 3 S TENSOR REMARK 3 S11: 0.1614 S12: 1.1551 S13: -0.2365 REMARK 3 S21: -0.7501 S22: -0.3007 S23: 0.7616 REMARK 3 S31: -0.3157 S32: -0.8370 S33: 0.1623 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 536 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.5312 23.1639 -4.3816 REMARK 3 T TENSOR REMARK 3 T11: 0.4568 T22: 0.2458 REMARK 3 T33: 0.3646 T12: -0.0521 REMARK 3 T13: 0.0071 T23: -0.0794 REMARK 3 L TENSOR REMARK 3 L11: 7.2047 L22: 5.9383 REMARK 3 L33: 7.7535 L12: 0.6384 REMARK 3 L13: -3.4295 L23: -2.2032 REMARK 3 S TENSOR REMARK 3 S11: -0.1615 S12: 0.5747 S13: -0.4813 REMARK 3 S21: -0.0164 S22: -0.1967 S23: 0.5001 REMARK 3 S31: 1.4403 S32: -0.5808 S33: 0.3563 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 537 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.1739 11.8277 5.8381 REMARK 3 T TENSOR REMARK 3 T11: 0.1438 T22: 0.0761 REMARK 3 T33: 0.1225 T12: 0.0082 REMARK 3 T13: 0.0124 T23: 0.0157 REMARK 3 L TENSOR REMARK 3 L11: 2.3943 L22: 2.7204 REMARK 3 L33: 3.6073 L12: 0.7273 REMARK 3 L13: 0.6059 L23: 0.7486 REMARK 3 S TENSOR REMARK 3 S11: -0.0221 S12: 0.0382 S13: -0.0662 REMARK 3 S21: -0.0921 S22: 0.0322 S23: 0.1181 REMARK 3 S31: -0.0283 S32: -0.0471 S33: -0.0106 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 6BH1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1000230702. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-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) : 1.0000 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 : 24685 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 27.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.73300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: 5E6H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 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 58.01400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.89300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.01400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.89300 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 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 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 GLY A 353 REMARK 465 PHE A 354 REMARK 465 GLU A 355 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 12 CG CD OE1 OE2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 THR A 30 OG1 CG2 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 GLU A 81 CG CD OE1 OE2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 GLN A 356 CG CD OE1 NE2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 GLU A 388 CG CD OE1 OE2 REMARK 470 ILE A 401 CG1 CG2 CD1 REMARK 470 GLU A 402 CG CD OE1 OE2 REMARK 470 GLU A 403 CG CD OE1 OE2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 LYS A 425 CG CD CE NZ REMARK 470 ASP A 426 CG OD1 OD2 REMARK 470 ARG A 428 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 ILE A 431 CG1 CG2 CD1 REMARK 470 LEU A 432 CG CD1 CD2 REMARK 470 GLU A 434 CG CD OE1 OE2 REMARK 470 GLU A 435 CG CD OE1 OE2 REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 GLN A 453 CG CD OE1 NE2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 GLN A 513 CG CD OE1 NE2 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 470 LEU A 532 CG CD1 CD2 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 O HOH A 740 O HOH A 838 2.18 REMARK 500 O HOH A 843 O HOH A 851 2.18 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 PHE A 477 -7.12 81.67 REMARK 500 VAL A 537 27.11 -142.50 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 92.9 REMARK 620 3 HIS A 571 NE2 84.6 87.4 REMARK 620 4 DQG A 601 N28 94.3 169.2 101.2 REMARK 620 5 HOH A 727 O 96.5 80.9 168.4 90.3 REMARK 620 6 HOH A 757 O 177.9 85.9 93.6 87.1 85.0 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 DQG 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 EDO A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 605 DBREF 6BH1 A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6BH1 A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6BH1 HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6BH1 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 DQG A 601 29 HET MN A 602 1 HET DMS A 603 4 HET EDO A 604 4 HET EDO A 605 4 HETNAM DQG 2-{(S)-(2-CHLOROPHENYL)[2-(PIPERIDIN-1-YL) HETNAM 2 DQG ETHOXY]METHYL}-1H-PYRROLO[3,2-B]PYRIDINE-7-CARBOXYLIC HETNAM 3 DQG ACID HETNAM MN MANGANESE (II) ION HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DQG C22 H24 CL N3 O3 FORMUL 3 MN MN 2+ FORMUL 4 DMS C2 H6 O S FORMUL 5 EDO 2(C2 H6 O2) FORMUL 7 HOH *160(H2 O) HELIX 1 AA1 GLU A 27 THR A 30 5 4 HELIX 2 AA2 ASP A 31 GLU A 44 1 14 HELIX 3 AA3 LEU A 363 ASN A 379 1 17 HELIX 4 AA4 PRO A 381 VAL A 385 5 5 HELIX 5 AA5 PRO A 386 SER A 400 1 15 HELIX 6 AA6 SER A 415 GLY A 419 1 5 HELIX 7 AA7 LEU A 432 GLU A 434 5 3 HELIX 8 AA8 GLU A 435 LEU A 440 1 6 HELIX 9 AA9 ASN A 444 MET A 448 5 5 HELIX 10 AB1 GLU A 485 SER A 489 5 5 HELIX 11 AB2 PRO A 507 HIS A 509 5 3 HELIX 12 AB3 ALA A 510 ALA A 522 1 13 HELIX 13 AB4 PRO A 523 SER A 528 1 6 HELIX 14 AB5 PRO A 530 GLN A 535 1 6 HELIX 15 AB6 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 NE2 HIS A 483 MN MN A 602 1555 1555 2.15 LINK OE1 GLU A 485 MN MN A 602 1555 1555 2.19 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.22 LINK N28 DQG A 601 MN MN A 602 1555 1555 2.25 LINK MN MN A 602 O HOH A 727 1555 1555 2.24 LINK MN MN A 602 O HOH A 757 1555 1555 1.85 SITE 1 AC1 17 TYR A 409 ALA A 411 ASP A 412 TRP A 470 SITE 2 AC1 17 TYR A 472 SER A 479 PHE A 480 CYS A 481 SITE 3 AC1 17 HIS A 483 ASN A 493 LYS A 501 TRP A 503 SITE 4 AC1 17 HIS A 571 MN A 602 EDO A 605 HOH A 757 SITE 5 AC1 17 HOH A 759 SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 DQG A 601 SITE 2 AC2 6 HOH A 727 HOH A 757 SITE 1 AC3 5 ALA A 357 MET A 384 SER A 508 PRO A 567 SITE 2 AC3 5 HOH A 752 SITE 1 AC4 2 HIS A 496 HOH A 800 SITE 1 AC5 5 LYS A 45 HIS A 509 TYR A 553 DQG A 601 SITE 2 AC5 5 HOH A 814 CRYST1 116.028 61.786 46.643 90.00 92.47 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 0.008619 0.000000 0.000373 0.00000 SCALE2 0.000000 0.016185 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021459 0.00000