HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 20-MAR-16 5IVE
TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N8 ( 5-METHYL-7-OXO-6-
TITLE 2 (PROPAN-2-YL)-4,7-DIHYDROPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE)
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.-;
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 C-PLUS
KEYWDS DEMETHYLASE INHIBITION, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.R.HORTON,X.CHENG
REVDAT 3 27-SEP-23 5IVE 1 REMARK
REVDAT 2 03-AUG-16 5IVE 1 JRNL
REVDAT 1 27-JUL-16 5IVE 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. 1.78 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) : 1.78
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.02
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.1
REMARK 3 NUMBER OF REFLECTIONS : 30863
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.176
REMARK 3 R VALUE (WORKING SET) : 0.175
REMARK 3 FREE R VALUE : 0.206
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020
REMARK 3 FREE R VALUE TEST SET COUNT : 1549
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 33.0301 - 3.9638 1.00 2851 140 0.1565 0.1750
REMARK 3 2 3.9638 - 3.1469 1.00 2779 153 0.1454 0.1920
REMARK 3 3 3.1469 - 2.7494 1.00 2748 157 0.1629 0.1795
REMARK 3 4 2.7494 - 2.4981 1.00 2789 148 0.1705 0.2074
REMARK 3 5 2.4981 - 2.3191 1.00 2780 149 0.1822 0.2159
REMARK 3 6 2.3191 - 2.1824 1.00 2774 140 0.1844 0.2219
REMARK 3 7 2.1824 - 2.0731 1.00 2728 150 0.1924 0.2427
REMARK 3 8 2.0731 - 1.9829 0.99 2746 139 0.2061 0.2406
REMARK 3 9 1.9829 - 1.9066 0.96 2647 134 0.2298 0.2598
REMARK 3 10 1.9066 - 1.8408 0.89 2425 135 0.2629 0.2482
REMARK 3 11 1.8408 - 1.7832 0.74 2047 104 0.2618 0.2850
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) : 0.180
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.740
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 : 0.006 2482
REMARK 3 ANGLE : 0.807 3407
REMARK 3 CHIRALITY : 0.050 356
REMARK 3 PLANARITY : 0.006 447
REMARK 3 DIHEDRAL : 12.703 1433
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 4
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 359 )
REMARK 3 ORIGIN FOR THE GROUP (A): -21.6285 14.6669 8.9206
REMARK 3 T TENSOR
REMARK 3 T11: 0.1784 T22: 0.1277
REMARK 3 T33: 0.0410 T12: -0.0316
REMARK 3 T13: 0.0084 T23: 0.0587
REMARK 3 L TENSOR
REMARK 3 L11: 2.7233 L22: 3.4543
REMARK 3 L33: 2.5143 L12: -0.1414
REMARK 3 L13: 0.0188 L23: 0.7828
REMARK 3 S TENSOR
REMARK 3 S11: 0.0548 S12: -0.0981 S13: 0.0707
REMARK 3 S21: -0.0141 S22: 0.0610 S23: -0.0728
REMARK 3 S31: -0.1782 S32: 0.0581 S33: -0.1103
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 399 )
REMARK 3 ORIGIN FOR THE GROUP (A): -29.3625 19.7370 22.9943
REMARK 3 T TENSOR
REMARK 3 T11: 0.1582 T22: 0.1600
REMARK 3 T33: 0.1158 T12: 0.0433
REMARK 3 T13: 0.0359 T23: -0.0070
REMARK 3 L TENSOR
REMARK 3 L11: 2.5722 L22: 4.4075
REMARK 3 L33: 3.8193 L12: 1.3985
REMARK 3 L13: -0.1815 L23: 0.1164
REMARK 3 S TENSOR
REMARK 3 S11: 0.0080 S12: -0.2301 S13: 0.1351
REMARK 3 S21: 0.4799 S22: -0.0218 S23: 0.1484
REMARK 3 S31: -0.1408 S32: -0.2494 S33: 0.0099
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 400 THROUGH 469 )
REMARK 3 ORIGIN FOR THE GROUP (A): -12.3724 22.1448 6.4096
REMARK 3 T TENSOR
REMARK 3 T11: 0.2105 T22: 0.2296
REMARK 3 T33: 0.2461 T12: -0.0830
REMARK 3 T13: 0.0496 T23: -0.0264
REMARK 3 L TENSOR
REMARK 3 L11: 2.7725 L22: 1.7931
REMARK 3 L33: 2.1704 L12: -1.5438
REMARK 3 L13: -0.2121 L23: 0.5083
REMARK 3 S TENSOR
REMARK 3 S11: 0.1213 S12: -0.0283 S13: 0.4803
REMARK 3 S21: -0.0951 S22: 0.0305 S23: -0.2692
REMARK 3 S31: -0.3726 S32: 0.4291 S33: -0.1459
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 588 )
REMARK 3 ORIGIN FOR THE GROUP (A): -27.8306 14.5383 3.7601
REMARK 3 T TENSOR
REMARK 3 T11: 0.1324 T22: 0.0735
REMARK 3 T33: 0.1073 T12: -0.0183
REMARK 3 T13: 0.0149 T23: 0.0164
REMARK 3 L TENSOR
REMARK 3 L11: 2.1864 L22: 2.1654
REMARK 3 L33: 3.5430 L12: -0.0717
REMARK 3 L13: 0.9859 L23: 0.4400
REMARK 3 S TENSOR
REMARK 3 S11: 0.0309 S12: 0.0533 S13: -0.0213
REMARK 3 S21: -0.2018 S22: -0.0019 S23: 0.1749
REMARK 3 S31: 0.0235 S32: -0.1890 S33: -0.0273
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 5IVE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-16.
REMARK 100 THE DEPOSITION ID IS D_1000219494.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-DEC-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) : 1.00000
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 : 30877
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.783
REMARK 200 RESOLUTION RANGE LOW (A) : 33.024
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4
REMARK 200 DATA REDUNDANCY : 3.900
REMARK 200 R MERGE (I) : 0.11800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85
REMARK 200 COMPLETENESS FOR SHELL (%) : 77.4
REMARK 200 DATA REDUNDANCY IN SHELL : 2.20
REMARK 200 R MERGE FOR SHELL (I) : 0.76600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: 5E6H
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.15
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 58.55200
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.03700
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.55200
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.03700
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 863 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 877 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 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 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 THR A 84 OG1 CG2
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 GLN A 356 CG CD OE1 NE2
REMARK 470 VAL A 358 CG1 CG2
REMARK 470 GLN A 364 CG CD OE1 NE2
REMARK 470 GLU A 388 CG CD OE1 OE2
REMARK 470 LYS A 392 CG CD CE NZ
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 ARG A 429 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 430 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 GLN A 453 CG CD OE1 NE2
REMARK 470 SER A 454 OG
REMARK 470 VAL A 455 CG1 CG2
REMARK 470 LYS A 467 CG CD CE NZ
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 LEU A 525 CG CD1 CD2
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 851 O HOH A 895 2.15
REMARK 500 O HOH A 879 O HOH A 882 2.18
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 GLN A 356 -131.36 65.65
REMARK 500 PHE A 477 -12.65 82.19
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLU A 355 GLN A 356 -144.11
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 83.8 88.2
REMARK 620 4 6E8 A 601 N16 89.3 168.4 102.8
REMARK 620 5 HOH A 797 O 173.8 90.4 97.8 84.5
REMARK 620 6 HOH A 812 O 95.6 86.5 174.6 82.5 83.3
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 6E8 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 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: 5IVF RELATED DB: PDB
REMARK 900 RELATED ID: 5IVJ 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 5IVE A 1 347 UNP P29375 KDM5A_HUMAN 1 87
DBREF 5IVE A 348 588 UNP P29375 KDM5A_HUMAN 348 588
SEQADV 5IVE HIS A -1 UNP P29375 EXPRESSION TAG
SEQADV 5IVE 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 6E8 A 601 16
HET MN A 602 1
HETNAM 6E8 5-METHYL-7-OXO-6-(PROPAN-2-YL)-4,7-DIHYDROPYRAZOLO[1,5-
HETNAM 2 6E8 A]PYRIMIDINE-3-CARBONITRILE
HETNAM MN MANGANESE (II) ION
FORMUL 2 6E8 C11 H12 N4 O
FORMUL 3 MN MN 2+
FORMUL 4 HOH *196(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 ASN A 78 MET A 83 1 6
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 400 1 15
HELIX 7 AA7 SER A 415 GLY A 419 1 5
HELIX 8 AA8 LEU A 432 SER A 441 1 10
HELIX 9 AA9 ASN A 444 MET A 448 5 5
HELIX 10 AB1 GLU A 485 SER A 489 5 5
HELIX 11 AB2 PRO A 507 HIS A 509 5 3
HELIX 12 AB3 ALA A 510 ALA A 522 1 13
HELIX 13 AB4 PRO A 523 SER A 528 1 6
HELIX 14 AB5 PRO A 530 GLN A 535 1 6
HELIX 15 AB6 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 2.31
LINK OE2 GLU A 485 MN MN A 602 1555 1555 2.14
LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.23
LINK N16 6E8 A 601 MN MN A 602 1555 1555 2.22
LINK MN MN A 602 O HOH A 797 1555 1555 2.11
LINK MN MN A 602 O HOH A 812 1555 1555 2.20
SITE 1 AC1 13 TYR A 409 GLY A 410 TYR A 472 SER A 479
SITE 2 AC1 13 PHE A 480 HIS A 483 LYS A 501 HIS A 571
SITE 3 AC1 13 ASN A 575 MN A 602 HOH A 776 HOH A 797
SITE 4 AC1 13 HOH A 812
SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 6E8 A 601
SITE 2 AC2 6 HOH A 797 HOH A 812
CRYST1 117.104 62.074 46.860 90.00 92.34 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 0.008539 0.000000 0.000349 0.00000
SCALE2 0.000000 0.016110 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021358 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
