HEADER OXIDOREDUCTASE/INHIBITOR 29-OCT-17 6BGW TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-CHLOROPHENYL)(2- TITLE 2 (4,4-DIFLUOROPIPERIDIN-1-YL)ETHOXY)METHYL)-1H-PYRROLO[3,2-B]PYRIDINE- TITLE 3 7-CARBOXYLIC ACID(COMPOUND N41) 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 6BGW 1 LINK REVDAT 3 01-JAN-20 6BGW 1 REMARK REVDAT 2 25-APR-18 6BGW 1 JRNL REVDAT 1 28-MAR-18 6BGW 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. 1.64 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) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 39550 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 : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1921 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 32.8903 - 3.9593 1.00 2834 138 0.1726 0.1887 REMARK 3 2 3.9593 - 3.1435 1.00 2751 146 0.1615 0.2123 REMARK 3 3 3.1435 - 2.7463 1.00 2749 135 0.1855 0.1883 REMARK 3 4 2.7463 - 2.4953 0.99 2737 148 0.1906 0.2032 REMARK 3 5 2.4953 - 2.3165 0.99 2755 141 0.1963 0.2123 REMARK 3 6 2.3165 - 2.1800 0.99 2700 151 0.1862 0.2268 REMARK 3 7 2.1800 - 2.0708 0.99 2701 138 0.1935 0.2457 REMARK 3 8 2.0708 - 1.9807 0.99 2699 140 0.1983 0.2211 REMARK 3 9 1.9807 - 1.9044 0.98 2689 134 0.2064 0.2354 REMARK 3 10 1.9044 - 1.8387 0.98 2685 144 0.2193 0.2296 REMARK 3 11 1.8387 - 1.7812 0.98 2698 119 0.2236 0.2476 REMARK 3 12 1.7812 - 1.7303 0.98 2665 148 0.2413 0.2457 REMARK 3 13 1.7303 - 1.6848 0.97 2647 140 0.2488 0.2830 REMARK 3 14 1.6848 - 1.6437 0.83 2319 99 0.2769 0.3072 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.350 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 2611 REMARK 3 ANGLE : 0.491 3567 REMARK 3 CHIRALITY : 0.046 365 REMARK 3 PLANARITY : 0.004 465 REMARK 3 DIHEDRAL : 9.688 1510 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 11 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.0757 4.6088 6.4655 REMARK 3 T TENSOR REMARK 3 T11: 0.1963 T22: 0.2000 REMARK 3 T33: 0.2384 T12: 0.0087 REMARK 3 T13: -0.0177 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 2.4531 L22: 2.9881 REMARK 3 L33: 2.2630 L12: 1.1395 REMARK 3 L13: 0.8343 L23: 0.9945 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: 0.2150 S13: -0.2734 REMARK 3 S21: 0.0462 S22: 0.1691 S23: -0.3467 REMARK 3 S31: 0.0457 S32: 0.4100 S33: -0.1574 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.3277 30.7489 12.6741 REMARK 3 T TENSOR REMARK 3 T11: 0.3366 T22: 0.2168 REMARK 3 T33: 0.3033 T12: 0.0610 REMARK 3 T13: -0.0242 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 5.1579 L22: 2.8901 REMARK 3 L33: 2.6251 L12: -1.0449 REMARK 3 L13: 0.3519 L23: 0.0904 REMARK 3 S TENSOR REMARK 3 S11: -0.3180 S12: -0.0465 S13: 0.9379 REMARK 3 S21: -0.0825 S22: 0.0553 S23: 0.4556 REMARK 3 S31: -0.4731 S32: -0.3644 S33: 0.2380 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.7951 19.9139 22.4570 REMARK 3 T TENSOR REMARK 3 T11: 0.2085 T22: 0.1632 REMARK 3 T33: 0.1465 T12: 0.0384 REMARK 3 T13: 0.0371 T23: -0.0141 REMARK 3 L TENSOR REMARK 3 L11: 2.7513 L22: 3.4816 REMARK 3 L33: 3.6227 L12: 1.7991 REMARK 3 L13: 0.5735 L23: 0.6441 REMARK 3 S TENSOR REMARK 3 S11: -0.0076 S12: -0.2566 S13: 0.0884 REMARK 3 S21: 0.4069 S22: -0.0807 S23: 0.1456 REMARK 3 S31: 0.0391 S32: -0.1850 S33: 0.0774 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2594 21.8505 3.8564 REMARK 3 T TENSOR REMARK 3 T11: 0.2082 T22: 0.2886 REMARK 3 T33: 0.2795 T12: -0.0804 REMARK 3 T13: 0.0283 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 1.9361 L22: 1.3830 REMARK 3 L33: 1.3230 L12: -0.9600 REMARK 3 L13: -0.4323 L23: 0.6063 REMARK 3 S TENSOR REMARK 3 S11: 0.0479 S12: 0.1635 S13: 0.2412 REMARK 3 S21: -0.0841 S22: 0.0489 S23: -0.2707 REMARK 3 S31: -0.2425 S32: 0.3713 S33: -0.0739 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 460 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.3687 14.8057 3.4470 REMARK 3 T TENSOR REMARK 3 T11: 0.1512 T22: 0.1219 REMARK 3 T33: 0.1439 T12: 0.0011 REMARK 3 T13: 0.0099 T23: 0.0135 REMARK 3 L TENSOR REMARK 3 L11: 1.6906 L22: 1.5188 REMARK 3 L33: 2.1035 L12: -0.0527 REMARK 3 L13: 0.3162 L23: 0.4606 REMARK 3 S TENSOR REMARK 3 S11: -0.0046 S12: 0.1224 S13: -0.0257 REMARK 3 S21: -0.0359 S22: -0.0268 S23: 0.1095 REMARK 3 S31: -0.0822 S32: -0.0987 S33: 0.0276 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 6BGW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230652. 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 : 39550 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 32.884 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.17700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.81400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 44.56 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 58.28850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.91250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.28850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.91250 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 870 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 ARG A 345 REMARK 465 VAL A 346 REMARK 465 ARG A 347 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 LYS A 66 CG CD CE NZ REMARK 470 ARG A 69 CG CD NE CZ NH1 NH2 REMARK 470 PRO A 348 CG CD REMARK 470 ARG A 349 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 350 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 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 LYS A 467 CG CD CE NZ 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 477 -8.07 81.26 REMARK 500 VAL A 537 34.78 -141.14 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 95.3 REMARK 620 3 HIS A 571 NE2 83.8 86.7 REMARK 620 4 DKS A 601 N28 89.4 168.4 104.4 REMARK 620 5 HOH A 763 O 93.3 80.5 166.6 88.6 REMARK 620 6 HOH A 817 O 177.9 86.7 95.6 88.7 87.7 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 DKS 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 GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 608 DBREF 6BGW A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6BGW A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6BGW HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6BGW 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 DKS A 601 31 HET MN A 602 1 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET DMS A 608 4 HETNAM DKS 2-{(S)-(2-CHLOROPHENYL)[2-(4,4-DIFLUOROPIPERIDIN-1-YL) HETNAM 2 DKS ETHOXY]METHYL}-1H-PYRROLO[3,2-B]PYRIDINE-7-CARBOXYLIC HETNAM 3 DKS ACID HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DKS C22 H22 CL F2 N3 O3 FORMUL 3 MN MN 2+ FORMUL 4 GOL 5(C3 H8 O3) FORMUL 9 DMS C2 H6 O S FORMUL 10 HOH *203(H2 O) HELIX 1 AA1 ASP A 31 GLU A 44 1 14 HELIX 2 AA2 LEU A 80 THR A 84 5 5 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 GLU A 434 5 3 HELIX 8 AA8 GLU A 435 SER A 441 1 7 HELIX 9 AA9 ASN A 444 MET A 448 5 5 HELIX 10 AB1 SER A 454 ASN A 460 1 7 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 GLU A 527 5 5 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 THR A 555 N TRP A 503 LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.27 LINK OE2 GLU A 485 MN MN A 602 1555 1555 2.05 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.28 LINK N28 DKS A 601 MN MN A 602 1555 1555 2.25 LINK MN MN A 602 O HOH A 763 1555 1555 2.27 LINK MN MN A 602 O HOH A 817 1555 1555 2.17 SITE 1 AC1 16 ARG A 73 TYR A 409 ALA A 411 ASP A 412 SITE 2 AC1 16 TRP A 470 TYR A 472 PHE A 480 CYS A 481 SITE 3 AC1 16 HIS A 483 ASN A 493 LYS A 501 TRP A 503 SITE 4 AC1 16 HIS A 571 MN A 602 HOH A 735 HOH A 817 SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 DKS A 601 SITE 2 AC2 6 HOH A 763 HOH A 817 SITE 1 AC3 9 MET A 380 PRO A 381 GLU A 485 ASP A 486 SITE 2 AC3 9 HIS A 487 TRP A 488 HOH A 704 HOH A 720 SITE 3 AC3 9 HOH A 779 SITE 1 AC4 4 GLU A 23 PRO A 53 HOH A 702 HOH A 748 SITE 1 AC5 6 GLU A 81 VAL A 398 ILE A 539 MET A 540 SITE 2 AC5 6 ASN A 541 HOH A 789 SITE 1 AC6 1 VAL A 455 SITE 1 AC7 7 LYS A 45 ARG A 73 HIS A 509 LEU A 536 SITE 2 AC7 7 TYR A 553 HOH A 762 HOH A 857 SITE 1 AC8 4 GLU A 64 VAL A 65 LYS A 66 ARG A 429 CRYST1 116.577 61.825 46.758 90.00 92.13 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008578 0.000000 0.000319 0.00000 SCALE2 0.000000 0.016175 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021401 0.00000