HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 21-MAR-16 5IVJ TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N11 [3-({1-[2-(4,4- TITLE 2 DIFLUOROPIPERIDIN-1-YL)ETHYL]-5-FLUORO-1H-INDAZOL-3-YL}AMINO) TITLE 3 PYRIDINE-4-CARBOXYLIC ACID] COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LINKED KDM5A JMJ DOMAIN, UNP RESIDUES 1-87 AND 348-588; COMPND 5 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 6 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2; COMPND 7 EC: 1.14.11.-,1.14.11.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: 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 CPLUS KEYWDS DEMETHYLASE INHIBITION, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 27-SEP-23 5IVJ 1 REMARK LINK REVDAT 2 03-AUG-16 5IVJ 1 JRNL REVDAT 1 27-JUL-16 5IVJ 0 JRNL AUTH J.R.HORTON,X.LIU,M.GALE,L.WU,J.R.SHANKS,X.ZHANG,P.J.WEBBER, JRNL AUTH 2 J.S.BELL,S.C.KALES,B.T.MOTT,G.RAI,D.J.JANSEN,M.J.HENDERSON, JRNL AUTH 3 D.J.URBAN,M.D.HALL,A.SIMEONOV,D.J.MALONEY,M.A.JOHNS,H.FU, JRNL AUTH 4 A.JADHAV,P.M.VERTINO,Q.YAN,X.CHENG JRNL TITL STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLASE JRNL TITL 2 INHIBITION BY DIVERSE COMPOUNDS. JRNL REF CELL CHEM BIOL V. 23 769 2016 JRNL REFN ESSN 2451-9456 JRNL PMID 27427228 JRNL DOI 10.1016/J.CHEMBIOL.2016.06.006 REMARK 1 REMARK 1 REFERENCE 1 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. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 46849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.230 REMARK 3 FREE R VALUE TEST SET COUNT : 1980 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 32.9864 - 3.7793 1.00 3313 137 0.1452 0.1643 REMARK 3 2 3.7793 - 3.0004 1.00 3253 132 0.1471 0.1751 REMARK 3 3 3.0004 - 2.6213 1.00 3233 136 0.1595 0.1861 REMARK 3 4 2.6213 - 2.3817 1.00 3227 143 0.1684 0.2233 REMARK 3 5 2.3817 - 2.2110 1.00 3202 143 0.1507 0.1908 REMARK 3 6 2.2110 - 2.0807 1.00 3221 143 0.1503 0.1729 REMARK 3 7 2.0807 - 1.9765 1.00 3201 155 0.1506 0.1702 REMARK 3 8 1.9765 - 1.8905 1.00 3208 137 0.1632 0.2076 REMARK 3 9 1.8905 - 1.8177 1.00 3192 157 0.1656 0.2022 REMARK 3 10 1.8177 - 1.7550 1.00 3208 140 0.1640 0.1751 REMARK 3 11 1.7550 - 1.7001 1.00 3173 146 0.1833 0.2167 REMARK 3 12 1.7001 - 1.6515 1.00 3225 130 0.2013 0.2735 REMARK 3 13 1.6515 - 1.6080 0.99 3164 142 0.2160 0.2573 REMARK 3 14 1.6080 - 1.5688 0.95 3049 139 0.2351 0.2525 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.560 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 : 0.015 2482 REMARK 3 ANGLE : 1.208 3396 REMARK 3 CHIRALITY : 0.084 345 REMARK 3 PLANARITY : 0.009 440 REMARK 3 DIHEDRAL : 16.849 1440 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID 12:354) REMARK 3 ORIGIN FOR THE GROUP (A): -19.7510 12.6944 8.2741 REMARK 3 T TENSOR REMARK 3 T11: 0.0963 T22: 0.1123 REMARK 3 T33: 0.1464 T12: -0.0138 REMARK 3 T13: -0.0153 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 0.3554 L22: 0.4693 REMARK 3 L33: 0.9758 L12: 0.0683 REMARK 3 L13: -0.0457 L23: 0.2833 REMARK 3 S TENSOR REMARK 3 S11: -0.0410 S12: 0.0282 S13: -0.0255 REMARK 3 S21: 0.0741 S22: 0.0723 S23: -0.0320 REMARK 3 S31: -0.0202 S32: 0.1062 S33: 0.0082 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 355:383) REMARK 3 ORIGIN FOR THE GROUP (A): -26.3028 25.6479 24.0785 REMARK 3 T TENSOR REMARK 3 T11: 0.2439 T22: 0.1254 REMARK 3 T33: 0.1068 T12: 0.0107 REMARK 3 T13: -0.0090 T23: -0.0136 REMARK 3 L TENSOR REMARK 3 L11: 0.1244 L22: 0.1989 REMARK 3 L33: 0.1165 L12: 0.0010 REMARK 3 L13: 0.0483 L23: -0.0563 REMARK 3 S TENSOR REMARK 3 S11: -0.0286 S12: -0.1479 S13: 0.1095 REMARK 3 S21: 0.3122 S22: 0.0391 S23: 0.0338 REMARK 3 S31: -0.2706 S32: -0.0153 S33: -0.0102 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 384:427) REMARK 3 ORIGIN FOR THE GROUP (A): -26.1830 20.5773 14.2978 REMARK 3 T TENSOR REMARK 3 T11: 0.1613 T22: 0.0970 REMARK 3 T33: 0.1208 T12: -0.0017 REMARK 3 T13: 0.0181 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.2400 L22: 0.5328 REMARK 3 L33: 0.7093 L12: -0.0652 REMARK 3 L13: 0.2090 L23: 0.4744 REMARK 3 S TENSOR REMARK 3 S11: -0.0836 S12: -0.0059 S13: 0.0818 REMARK 3 S21: 0.0482 S22: 0.0945 S23: -0.0238 REMARK 3 S31: -0.1320 S32: -0.0031 S33: 0.0110 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 428:470) REMARK 3 ORIGIN FOR THE GROUP (A): -4.8366 18.9291 3.9954 REMARK 3 T TENSOR REMARK 3 T11: 0.1099 T22: 0.3185 REMARK 3 T33: 0.2158 T12: -0.0719 REMARK 3 T13: 0.0358 T23: -0.0347 REMARK 3 L TENSOR REMARK 3 L11: 0.4802 L22: 1.1596 REMARK 3 L33: 0.5117 L12: -0.3258 REMARK 3 L13: 0.0843 L23: 0.3783 REMARK 3 S TENSOR REMARK 3 S11: 0.1080 S12: -0.0344 S13: 0.0468 REMARK 3 S21: -0.1091 S22: 0.1017 S23: -0.2477 REMARK 3 S31: -0.2759 S32: 0.4108 S33: 0.2578 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 471:588) REMARK 3 ORIGIN FOR THE GROUP (A): -28.0516 14.3763 3.6944 REMARK 3 T TENSOR REMARK 3 T11: 0.0933 T22: 0.0756 REMARK 3 T33: 0.0760 T12: -0.0109 REMARK 3 T13: -0.0009 T23: 0.0038 REMARK 3 L TENSOR REMARK 3 L11: 0.5381 L22: 0.6721 REMARK 3 L33: 0.7705 L12: -0.3415 REMARK 3 L13: -0.0601 L23: 0.1848 REMARK 3 S TENSOR REMARK 3 S11: 0.0183 S12: 0.0107 S13: -0.0525 REMARK 3 S21: 0.0390 S22: -0.0055 S23: 0.0660 REMARK 3 S31: -0.0277 S32: -0.0244 S33: 0.0522 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 5IVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219500. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-15 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 : 46861 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.569 REMARK 200 RESOLUTION RANGE LOW (A) : 32.979 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.88500 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 (%): 45.18 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 58.27800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.25800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.27800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.25800 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 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 897 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 907 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 ALA A 11 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 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 12 CG CD OE1 OE2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 ASP A 56 CG OD1 OD2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLN A 356 CG CD OE1 NE2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 ASP A 376 CG OD1 OD2 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 ARG A 428 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 LYS A 467 CG CD CE NZ REMARK 470 ASP A 486 CG OD1 OD2 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 882 O HOH A 929 2.05 REMARK 500 O HOH A 929 O HOH A 937 2.14 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 ALA A 357 89.24 -158.73 REMARK 500 PHE A 477 -6.25 80.50 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 OE2 99.0 REMARK 620 3 HIS A 571 NE2 83.7 85.4 REMARK 620 4 6ED A 601 N07 88.0 170.8 101.3 REMARK 620 5 HOH A 732 O 93.6 83.2 167.8 90.5 REMARK 620 6 HOH A 741 O 174.2 86.4 94.8 86.9 89.1 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 6ED 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ISL RELATED DB: PDB REMARK 900 RELATED ID: 5IVB RELATED DB: PDB REMARK 900 RELATED ID: 5IVC RELATED DB: PDB REMARK 900 RELATED ID: 5IVE RELATED DB: PDB REMARK 900 RELATED ID: 5IVF RELATED DB: PDB REMARK 900 RELATED ID: 5IVV RELATED DB: PDB REMARK 900 RELATED ID: 5IVY RELATED DB: PDB REMARK 900 RELATED ID: 5IW0 RELATED DB: PDB REMARK 900 RELATED ID: 5IWF RELATED DB: PDB DBREF 5IVJ A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 5IVJ A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 5IVJ HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 5IVJ 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 6ED A 601 40 HET MN A 602 1 HET GOL A 603 6 HET DMS A 604 4 HETNAM 6ED 3-({1-[2-(4,4-DIFLUOROPIPERIDIN-1-YL)ETHYL]-5-FLUORO- HETNAM 2 6ED 1H-INDAZOL-3-YL}AMINO)PYRIDINE-4-CARBOXYLIC ACID HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 6ED C20 H20 F3 N5 O2 FORMUL 3 MN MN 2+ FORMUL 4 GOL C3 H8 O3 FORMUL 5 DMS C2 H6 O S FORMUL 6 HOH *259(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 399 1 14 HELIX 6 AA6 SER A 415 GLY A 419 1 5 HELIX 7 AA7 LEU A 432 SER A 441 1 10 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 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 TYR A 570 ASN A 575 -1 O GLY A 573 N PHE A 480 SHEET 3 AA3 4 LYS A 501 VAL A 506 -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 2.26 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 N07 6ED A 601 MN MN A 602 1555 1555 2.27 LINK MN MN A 602 O HOH A 732 1555 1555 2.22 LINK MN MN A 602 O HOH A 741 1555 1555 2.19 SITE 1 AC1 19 ARG A 73 GLN A 75 TYR A 409 ALA A 411 SITE 2 AC1 19 ASP A 412 TRP A 470 TYR A 472 PHE A 480 SITE 3 AC1 19 HIS A 483 ASN A 493 LYS A 501 TRP A 503 SITE 4 AC1 19 GLN A 535 LEU A 536 HIS A 571 MN A 602 SITE 5 AC1 19 HOH A 741 HOH A 842 HOH A 920 SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 6ED A 601 SITE 2 AC2 6 HOH A 732 HOH A 741 SITE 1 AC3 7 MET A 380 PRO A 381 GLU A 485 HIS A 487 SITE 2 AC3 7 HOH A 711 HOH A 776 HOH A 781 SITE 1 AC4 2 GLY A 367 ASP A 371 CRYST1 116.556 62.516 46.772 90.00 92.32 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 0.008580 0.000000 0.000347 0.00000 SCALE2 0.000000 0.015996 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021398 0.00000