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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
