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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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