HEADER OXIDOREDUCTASE/INHIBITOR 10-JUN-18 6DQD TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N53 I.E. 2-(5-([1,1'- TITLE 2 BIPHENYL]-3-YL)-4-(1-(2-(PIPERIDIN-1-YL)ETHOXY)ETHYL)-1H-PYRAZOL-1- TITLE 3 YL)ISONICOTINIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: LINKED KDM5A JMJ DOMAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 5 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2,HISTONE COMPND 6 DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1A, COMPND 7 RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2; COMPND 8 EC: 1.14.11.-; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KDM5A, JARID1A, RBBP2, RBP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: GOLD C-PLUS KEYWDS DEMETHYLASE INHIBITION, OXIDOREDUCTASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 11-OCT-23 6DQD 1 REMARK REVDAT 2 01-JAN-20 6DQD 1 REMARK REVDAT 1 12-JUN-19 6DQD 0 JRNL AUTH J.R.HORTON,X.LIU,C.B.WOODCOCK,J.SHANKS,X.ZHANG,G.RAI,B.MOTT, JRNL AUTH 2 D.J.JANSEN,S.KALES,M.J.HENDERSON,K.POHIDA,Y.FANG,X.HU, JRNL AUTH 3 A.JADHAV,D.MALONEY,M.D.HALL,A.SIMEONOV,H.FU,P.M.VERTINO, JRNL AUTH 4 X.CHENG JRNL TITL TO BE DETERMINED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.R.HORTON,X.LIU,M.GALE,L.WU,J.R.SHANKS,X.ZHANG,P.J.WEBBER, REMARK 1 AUTH 2 J.S.BELL,S.C.KALES,B.T.MOTT,G.RAI,D.J.JANSEN,M.J.HENDERSON, REMARK 1 AUTH 3 D.J.URBAN,M.D.HALL,A.SIMEONOV,D.J.MALONEY,M.A.JOHNS,H.FU, REMARK 1 AUTH 4 A.JADHAV,P.M.VERTINO,Q.YAN,X.CHENG REMARK 1 TITL STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLASE REMARK 1 TITL 2 INHIBITION BY DIVERSE COMPOUNDS. REMARK 1 REF CELL CHEM BIOL V. 23 769 2016 REMARK 1 REFN ESSN 2451-9456 REMARK 1 PMID 27427228 REMARK 1 DOI 10.1016/J.CHEMBIOL.2016.06.006 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.R.HORTON,A.ENGSTROM,E.L.ZOELLER,X.LIU,J.R.SHANKS,X.ZHANG, REMARK 1 AUTH 2 M.A.JOHNS,P.M.VERTINO,H.FU,X.CHENG REMARK 1 TITL CHARACTERIZATION OF A LINKED JUMONJI DOMAIN OF THE REMARK 1 TITL 2 KDM5/JARID1 FAMILY OF HISTONE H3 LYSINE 4 DEMETHYLASES. REMARK 1 REF J. BIOL. CHEM. V. 291 2631 2016 REMARK 1 REFN ESSN 1083-351X REMARK 1 PMID 26645689 REMARK 1 DOI 10.1074/JBC.M115.698449 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.R.HORTON,X.LIU,L.WU,K.ZHANG,J.SHANKS,X.ZHANG,G.RAI, REMARK 1 AUTH 2 B.T.MOTT,D.J.JANSEN,S.C.KALES,M.J.HENDERSON,K.POHIDA,Y.FANG, REMARK 1 AUTH 3 X.HU,A.JADHAV,D.J.MALONEY,M.D.HALL,A.SIMEONOV,H.FU, REMARK 1 AUTH 4 P.M.VERTINO,Q.YAN,X.CHENG REMARK 1 TITL INSIGHTS INTO THE ACTION OF INHIBITOR ENANTIOMERS AGAINST REMARK 1 TITL 2 HISTONE LYSINE DEMETHYLASE 5A. REMARK 1 REF J. MED. CHEM. V. 61 3193 2018 REMARK 1 REFN ISSN 1520-4804 REMARK 1 PMID 29537847 REMARK 1 DOI 10.1021/ACS.JMEDCHEM.8B00261 REMARK 2 REMARK 2 RESOLUTION. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 22831 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) : 0.189 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1159 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 30.9532 - 3.9712 1.00 2788 166 0.1633 0.1972 REMARK 3 2 3.9712 - 3.1530 1.00 2727 147 0.1541 0.1665 REMARK 3 3 3.1530 - 2.7547 1.00 2722 143 0.1797 0.2216 REMARK 3 4 2.7547 - 2.5030 1.00 2735 145 0.2025 0.2829 REMARK 3 5 2.5030 - 2.3237 1.00 2713 148 0.2159 0.2764 REMARK 3 6 2.3237 - 2.1867 1.00 2739 137 0.2242 0.2438 REMARK 3 7 2.1867 - 2.0772 1.00 2675 150 0.2482 0.2394 REMARK 3 8 2.0772 - 1.9868 0.94 2573 123 0.2786 0.2719 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.130 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 : 0.003 2536 REMARK 3 ANGLE : 0.628 3472 REMARK 3 CHIRALITY : 0.043 359 REMARK 3 PLANARITY : 0.005 452 REMARK 3 DIHEDRAL : 4.165 1964 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 12 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.3963 2.5854 8.4734 REMARK 3 T TENSOR REMARK 3 T11: 0.2450 T22: 0.1388 REMARK 3 T33: 0.2671 T12: 0.0269 REMARK 3 T13: -0.0280 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 7.2158 L22: 2.6493 REMARK 3 L33: 1.8599 L12: -0.3765 REMARK 3 L13: 0.4404 L23: 0.4717 REMARK 3 S TENSOR REMARK 3 S11: 0.0980 S12: 0.1123 S13: -0.4886 REMARK 3 S21: 0.1518 S22: 0.0012 S23: -0.4518 REMARK 3 S31: 0.2319 S32: 0.3417 S33: -0.1039 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 81 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7610 14.2569 8.0357 REMARK 3 T TENSOR REMARK 3 T11: 0.1489 T22: 0.1554 REMARK 3 T33: 0.1203 T12: -0.0329 REMARK 3 T13: 0.0038 T23: 0.0664 REMARK 3 L TENSOR REMARK 3 L11: 1.9461 L22: 2.7026 REMARK 3 L33: 1.7983 L12: -0.2418 REMARK 3 L13: -0.0022 L23: 0.8304 REMARK 3 S TENSOR REMARK 3 S11: 0.0380 S12: 0.0053 S13: 0.0368 REMARK 3 S21: -0.0123 S22: 0.0604 S23: -0.2892 REMARK 3 S31: -0.1067 S32: 0.1919 S33: -0.1012 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 82 THROUGH 362 ) REMARK 3 ORIGIN FOR THE GROUP (A): -34.7744 34.9899 13.9551 REMARK 3 T TENSOR REMARK 3 T11: 0.5912 T22: 0.3798 REMARK 3 T33: 0.5761 T12: 0.0374 REMARK 3 T13: -0.0508 T23: -0.0340 REMARK 3 L TENSOR REMARK 3 L11: 0.1233 L22: 0.4809 REMARK 3 L33: 2.0191 L12: -0.2368 REMARK 3 L13: 0.3463 L23: -0.8572 REMARK 3 S TENSOR REMARK 3 S11: 0.0652 S12: 0.2230 S13: 0.4777 REMARK 3 S21: -0.2049 S22: 0.0619 S23: 0.4470 REMARK 3 S31: -0.3387 S32: -0.4855 S33: -0.1003 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 363 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.0407 18.7354 22.7306 REMARK 3 T TENSOR REMARK 3 T11: 0.1703 T22: 0.1679 REMARK 3 T33: 0.1242 T12: 0.0182 REMARK 3 T13: 0.0453 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 2.3339 L22: 3.0974 REMARK 3 L33: 3.3896 L12: 0.9891 REMARK 3 L13: 0.3074 L23: 0.2052 REMARK 3 S TENSOR REMARK 3 S11: 0.0147 S12: -0.1808 S13: 0.0657 REMARK 3 S21: 0.3474 S22: -0.0308 S23: 0.1881 REMARK 3 S31: -0.0599 S32: -0.3286 S33: 0.0241 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 432 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.4514 26.5010 10.0631 REMARK 3 T TENSOR REMARK 3 T11: 0.3228 T22: 0.2983 REMARK 3 T33: 0.3799 T12: -0.1218 REMARK 3 T13: 0.0459 T23: -0.0649 REMARK 3 L TENSOR REMARK 3 L11: 3.0585 L22: 1.8781 REMARK 3 L33: 2.0915 L12: -1.4717 REMARK 3 L13: -0.3739 L23: -0.2037 REMARK 3 S TENSOR REMARK 3 S11: 0.1705 S12: 0.2111 S13: 1.0419 REMARK 3 S21: 0.0027 S22: 0.0628 S23: -0.5973 REMARK 3 S31: -0.4314 S32: 0.5381 S33: -0.1929 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -18.9722 16.3178 2.0872 REMARK 3 T TENSOR REMARK 3 T11: 0.1386 T22: 0.1133 REMARK 3 T33: 0.1326 T12: -0.0079 REMARK 3 T13: 0.0179 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 1.4372 L22: 1.0474 REMARK 3 L33: 1.8211 L12: 0.0010 REMARK 3 L13: 0.0148 L23: 0.2804 REMARK 3 S TENSOR REMARK 3 S11: 0.0359 S12: 0.2052 S13: 0.0671 REMARK 3 S21: -0.0911 S22: 0.0153 S23: -0.0897 REMARK 3 S31: -0.0980 S32: 0.1951 S33: -0.0438 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -28.7657 14.2236 3.7190 REMARK 3 T TENSOR REMARK 3 T11: 0.1373 T22: 0.1246 REMARK 3 T33: 0.1444 T12: -0.0027 REMARK 3 T13: 0.0177 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 1.0266 L22: 2.0559 REMARK 3 L33: 2.2858 L12: -0.0031 REMARK 3 L13: 0.5337 L23: 0.2100 REMARK 3 S TENSOR REMARK 3 S11: -0.0052 S12: 0.0818 S13: 0.0318 REMARK 3 S21: -0.1428 S22: 0.0155 S23: 0.1653 REMARK 3 S31: -0.0531 S32: -0.1545 S33: -0.0113 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 6DQD 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_1000234912. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : 22852 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.987 REMARK 200 RESOLUTION RANGE LOW (A) : 30.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.16100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 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 (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.94000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5IVB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 58.30500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.94950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.30500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.94950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 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 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 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 73 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 ARG A 349 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 350 CG CD OE1 OE2 REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 LYS A 392 CG CD CE NZ 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 ASP A 417 CG OD1 OD2 REMARK 470 LYS A 425 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 452 CG CD OE1 OE2 REMARK 470 ILE A 459 CG1 CG2 CD1 REMARK 470 ASN A 460 CG OD1 ND2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 GLN A 513 CG CD OE1 NE2 REMARK 470 GLU A 516 CG CD OE1 OE2 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 LEU A 532 CG CD1 CD2 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 -4.58 79.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 867 DISTANCE = 5.96 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 483 NE2 REMARK 620 2 GLU A 485 OE1 93.1 REMARK 620 3 HIS A 571 NE2 84.4 91.3 REMARK 620 4 H67 A 601 N06 90.8 166.7 101.7 REMARK 620 5 HOH A 748 O 174.0 92.8 96.5 83.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue H67 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 GOL 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 DMS A 606 DBREF 6DQD A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6DQD A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6DQD HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6DQD 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 H67 A 601 37 HET MN A 602 1 HET GOL A 603 6 HET GOL A 604 6 HET DMS A 605 4 HET DMS A 606 4 HETNAM H67 2-[5-([1,1'-BIPHENYL]-3-YL)-4-{(1S)-1-[2-(PIPERIDIN-1- HETNAM 2 H67 YL)ETHOXY]ETHYL}-1H-PYRAZOL-1-YL]PYRIDINE-4-CARBOXYLIC HETNAM 3 H67 ACID HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 H67 C30 H32 N4 O3 FORMUL 3 MN MN 2+ FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 DMS 2(C2 H6 O S) FORMUL 8 HOH *167(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 VAL A 455 ASN A 460 1 6 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 GLY A 410 O VAL A 473 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 THR A 555 N TRP A 503 LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.26 LINK OE1 GLU A 485 MN MN A 602 1555 1555 2.13 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.22 LINK N06 H67 A 601 MN MN A 602 1555 1555 2.27 LINK MN MN A 602 O HOH A 748 1555 1555 1.97 SITE 1 AC1 17 GLN A 75 TYR A 409 ALA A 411 ASP A 412 SITE 2 AC1 17 TRP A 470 TYR A 472 PHE A 480 CYS A 481 SITE 3 AC1 17 HIS A 483 GLU A 485 LYS A 501 TRP A 503 SITE 4 AC1 17 HIS A 571 MN A 602 DMS A 605 HOH A 748 SITE 5 AC1 17 HOH A 808 SITE 1 AC2 5 HIS A 483 GLU A 485 HIS A 571 H67 A 601 SITE 2 AC2 5 HOH A 748 SITE 1 AC3 7 SER A 375 ASN A 379 MET A 380 PRO A 381 SITE 2 AC3 7 ASP A 486 HIS A 487 HOH A 768 SITE 1 AC4 5 SER A 399 ILE A 539 MET A 540 ASN A 541 SITE 2 AC4 5 HOH A 705 SITE 1 AC5 4 TYR A 472 GLU A 485 ASN A 585 H67 A 601 SITE 1 AC6 5 GLY A 353 ALA A 357 MET A 384 SER A 508 SITE 2 AC6 5 ARG A 568 CRYST1 116.610 61.899 46.649 90.00 92.17 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 0.008576 0.000000 0.000325 0.00000 SCALE2 0.000000 0.016155 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021452 0.00000