HEADER OXIDOREDUCTASE/INHIBITOR 29-OCT-17 6BH0 TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR (R)-2-((2- TITLE 2 CHLOROPHENYL)(2-(PIPERIDIN-1-YL)ETHOXY)METHYL)-1L2-PYRROLO[3,2- TITLE 3 B]PYRIDINE-7-CARBOXYLIC ACID (COMPOUND N51) 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,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-OXIDOREDUCTASE INHIBITOR KEYWDS 2 COMPLEX, OXIDOREDUCTASE, OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 4 04-OCT-23 6BH0 1 LINK REVDAT 3 01-JAN-20 6BH0 1 REMARK REVDAT 2 25-APR-18 6BH0 1 JRNL REVDAT 1 28-MAR-18 6BH0 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. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_2863 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 23077 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 1161 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 32.9517 - 3.9681 1.00 2819 153 0.1601 0.2050 REMARK 3 2 3.9681 - 3.1504 1.00 2753 145 0.1627 0.1828 REMARK 3 3 3.1504 - 2.7524 1.00 2750 150 0.1927 0.2113 REMARK 3 4 2.7524 - 2.5009 1.00 2758 141 0.2076 0.2611 REMARK 3 5 2.5009 - 2.3217 1.00 2769 141 0.2105 0.2396 REMARK 3 6 2.3217 - 2.1848 1.00 2741 154 0.2113 0.2166 REMARK 3 7 2.1848 - 2.0754 1.00 2721 139 0.2355 0.2948 REMARK 3 8 2.0754 - 1.9851 0.95 2605 138 0.2623 0.2591 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) : 22.450 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 2392 REMARK 3 ANGLE : 0.477 3278 REMARK 3 CHIRALITY : 0.041 342 REMARK 3 PLANARITY : 0.004 425 REMARK 3 DIHEDRAL : 15.617 1380 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 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.4774 4.6513 6.7903 REMARK 3 T TENSOR REMARK 3 T11: 0.2358 T22: 0.2328 REMARK 3 T33: 0.2890 T12: 0.0133 REMARK 3 T13: -0.0215 T23: 0.0035 REMARK 3 L TENSOR REMARK 3 L11: 3.3171 L22: 3.7075 REMARK 3 L33: 2.8521 L12: 1.1568 REMARK 3 L13: 1.5158 L23: 1.3083 REMARK 3 S TENSOR REMARK 3 S11: -0.0338 S12: 0.2150 S13: -0.3264 REMARK 3 S21: 0.1305 S22: 0.2732 S23: -0.5828 REMARK 3 S31: 0.0336 S32: 0.6856 S33: -0.2415 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 414 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.9186 23.7418 18.1346 REMARK 3 T TENSOR REMARK 3 T11: 0.2573 T22: 0.1516 REMARK 3 T33: 0.1596 T12: 0.0375 REMARK 3 T13: 0.0371 T23: -0.0268 REMARK 3 L TENSOR REMARK 3 L11: 3.3610 L22: 3.1770 REMARK 3 L33: 3.9184 L12: 0.9257 REMARK 3 L13: 0.0091 L23: 0.1411 REMARK 3 S TENSOR REMARK 3 S11: -0.0738 S12: -0.0684 S13: 0.2989 REMARK 3 S21: 0.2802 S22: 0.0051 S23: 0.2098 REMARK 3 S31: -0.2436 S32: -0.2155 S33: 0.0513 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 415 THROUGH 447 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.6113 19.6829 7.9045 REMARK 3 T TENSOR REMARK 3 T11: 0.2976 T22: 0.5095 REMARK 3 T33: 0.4678 T12: -0.1083 REMARK 3 T13: 0.0406 T23: -0.1145 REMARK 3 L TENSOR REMARK 3 L11: 4.6213 L22: 1.3307 REMARK 3 L33: 1.9130 L12: -0.2417 REMARK 3 L13: 0.4946 L23: -0.2226 REMARK 3 S TENSOR REMARK 3 S11: 0.0460 S12: -0.4098 S13: 0.3743 REMARK 3 S21: 0.2622 S22: 0.2727 S23: -0.7553 REMARK 3 S31: -0.4471 S32: 0.8326 S33: -0.2741 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 448 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.3892 17.0360 5.1426 REMARK 3 T TENSOR REMARK 3 T11: 0.1909 T22: 0.1368 REMARK 3 T33: 0.1293 T12: -0.0088 REMARK 3 T13: 0.0197 T23: 0.0295 REMARK 3 L TENSOR REMARK 3 L11: 1.8617 L22: 2.2093 REMARK 3 L33: 1.6840 L12: -0.1146 REMARK 3 L13: 1.1953 L23: 1.2641 REMARK 3 S TENSOR REMARK 3 S11: 0.0042 S12: 0.1724 S13: 0.0772 REMARK 3 S21: -0.1052 S22: 0.0229 S23: -0.1452 REMARK 3 S31: -0.0707 S32: 0.2712 S33: -0.0233 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.3302 10.1473 -5.1298 REMARK 3 T TENSOR REMARK 3 T11: 0.2653 T22: 0.2613 REMARK 3 T33: 0.2842 T12: -0.0223 REMARK 3 T13: -0.0564 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 6.3419 L22: 9.6871 REMARK 3 L33: 8.5277 L12: -6.8081 REMARK 3 L13: -5.8599 L23: 4.0869 REMARK 3 S TENSOR REMARK 3 S11: 0.1649 S12: 0.7498 S13: -0.0287 REMARK 3 S21: -0.5873 S22: -0.0369 S23: 0.5615 REMARK 3 S31: -0.1540 S32: -0.6109 S33: -0.1179 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 548 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.7842 17.5679 -0.4180 REMARK 3 T TENSOR REMARK 3 T11: 0.2730 T22: 0.2467 REMARK 3 T33: 0.2697 T12: -0.0057 REMARK 3 T13: 0.0145 T23: -0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.9748 L22: 8.1065 REMARK 3 L33: 2.8588 L12: 0.6868 REMARK 3 L13: 0.1276 L23: -3.6911 REMARK 3 S TENSOR REMARK 3 S11: -0.0193 S12: 0.0072 S13: -0.0139 REMARK 3 S21: -0.4435 S22: 0.1093 S23: 0.4477 REMARK 3 S31: -0.0740 S32: -0.2834 S33: -0.0990 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 549 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.3631 12.2719 6.2554 REMARK 3 T TENSOR REMARK 3 T11: 0.1737 T22: 0.0981 REMARK 3 T33: 0.0933 T12: -0.0016 REMARK 3 T13: 0.0176 T23: 0.0163 REMARK 3 L TENSOR REMARK 3 L11: 2.5758 L22: 2.8856 REMARK 3 L33: 3.0064 L12: 0.4029 REMARK 3 L13: 1.0804 L23: 1.0769 REMARK 3 S TENSOR REMARK 3 S11: -0.0086 S12: 0.0288 S13: -0.1066 REMARK 3 S21: -0.0587 S22: 0.0231 S23: -0.0965 REMARK 3 S31: 0.0233 S32: 0.1495 S33: -0.0085 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 6BH0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230698. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-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 : 23086 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.985 REMARK 200 RESOLUTION RANGE LOW (A) : 32.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.64900 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: 5E6H 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 58.40650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.97700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.40650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.97700 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 ASP A 426 REMARK 465 GLY A 427 REMARK 465 ARG A 428 REMARK 465 ARG A 429 REMARK 465 LYS A 430 REMARK 465 GLN A 453 REMARK 465 SER A 454 REMARK 465 VAL A 455 REMARK 465 LEU A 456 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 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 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 PHE A 354 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLN A 364 CG CD OE1 NE2 REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 ILE A 401 CG1 CG2 CD1 REMARK 470 GLU A 402 CG CD OE1 OE2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 ASP A 417 CG OD1 OD2 REMARK 470 LYS A 425 CG CD CE NZ REMARK 470 LEU A 432 CG CD1 CD2 REMARK 470 GLU A 434 CG CD OE1 OE2 REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 VAL A 468 CG1 CG2 REMARK 470 GLN A 513 CG CD OE1 NE2 REMARK 470 ARG A 519 CG CD NE CZ NH1 NH2 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 470 GLU A 547 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 -6.78 80.58 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 OE2 95.6 REMARK 620 3 HIS A 571 NE2 85.0 86.0 REMARK 620 4 DO1 A 601 N28 89.7 169.6 103.4 REMARK 620 5 HOH A 744 O 93.9 81.9 167.6 88.9 REMARK 620 6 HOH A 745 O 178.8 85.1 96.1 89.5 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 DO1 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 DBREF 6BH0 A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6BH0 A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6BH0 HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6BH0 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 DO1 A 601 29 HET MN A 602 1 HET DMS A 603 4 HETNAM DO1 2-{(R)-(2-CHLOROPHENYL)[2-(PIPERIDIN-1-YL) HETNAM 2 DO1 ETHOXY]METHYL}-1H-PYRROLO[3,2-B]PYRIDINE-7-CARBOXYLIC HETNAM 3 DO1 ACID HETNAM MN MANGANESE (II) ION HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 DO1 C22 H24 CL N3 O3 FORMUL 3 MN MN 2+ FORMUL 4 DMS C2 H6 O S FORMUL 5 HOH *154(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 80 THR A 84 5 5 HELIX 4 AA4 LEU A 363 ASN A 379 1 17 HELIX 5 AA5 PRO A 381 VAL A 385 5 5 HELIX 6 AA6 PRO A 386 SER A 399 1 14 HELIX 7 AA7 SER A 415 GLY A 419 1 5 HELIX 8 AA8 LEU A 432 GLU A 434 5 3 HELIX 9 AA9 GLU A 435 LEU A 440 1 6 HELIX 10 AB1 ASN A 444 MET A 448 5 5 HELIX 11 AB2 GLU A 485 SER A 489 5 5 HELIX 12 AB3 PRO A 507 HIS A 509 5 3 HELIX 13 AB4 ALA A 510 ALA A 522 1 13 HELIX 14 AB5 PRO A 523 SER A 528 1 6 HELIX 15 AB6 PRO A 530 GLN A 535 1 6 HELIX 16 AB7 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 2.19 LINK OE2 GLU A 485 MN MN A 602 1555 1555 2.10 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.28 LINK N28 DO1 A 601 MN MN A 602 1555 1555 2.28 LINK MN MN A 602 O HOH A 744 1555 1555 2.17 LINK MN MN A 602 O HOH A 745 1555 1555 1.96 SITE 1 AC1 15 ARG A 73 GLN A 75 TYR A 409 ALA A 411 SITE 2 AC1 15 TRP A 470 TYR A 472 SER A 479 PHE A 480 SITE 3 AC1 15 HIS A 483 LYS A 501 TRP A 503 HIS A 571 SITE 4 AC1 15 MN A 602 HOH A 738 HOH A 745 SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 DO1 A 601 SITE 2 AC2 6 HOH A 744 HOH A 745 SITE 1 AC3 6 GLY A 353 GLN A 356 MET A 384 SER A 508 SITE 2 AC3 6 PRO A 567 HOH A 701 CRYST1 116.813 61.954 46.858 90.00 92.36 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 0.008561 0.000000 0.000353 0.00000 SCALE2 0.000000 0.016141 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021359 0.00000