HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 21-MAR-16 5IVJ
TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N11 [3-({1-[2-(4,4-
TITLE 2 DIFLUOROPIPERIDIN-1-YL)ETHYL]-5-FLUORO-1H-INDAZOL-3-YL}AMINO)
TITLE 3 PYRIDINE-4-CARBOXYLIC ACID]
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.-,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 CPLUS
KEYWDS DEMETHYLASE INHIBITION, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR
KEYWDS 2 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.R.HORTON,X.CHENG
REVDAT 3 27-SEP-23 5IVJ 1 REMARK LINK
REVDAT 2 03-AUG-16 5IVJ 1 JRNL
REVDAT 1 27-JUL-16 5IVJ 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. 1.57 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) : 1.57
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.98
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6
REMARK 3 NUMBER OF REFLECTIONS : 46849
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.160
REMARK 3 R VALUE (WORKING SET) : 0.159
REMARK 3 FREE R VALUE : 0.189
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.230
REMARK 3 FREE R VALUE TEST SET COUNT : 1980
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 32.9864 - 3.7793 1.00 3313 137 0.1452 0.1643
REMARK 3 2 3.7793 - 3.0004 1.00 3253 132 0.1471 0.1751
REMARK 3 3 3.0004 - 2.6213 1.00 3233 136 0.1595 0.1861
REMARK 3 4 2.6213 - 2.3817 1.00 3227 143 0.1684 0.2233
REMARK 3 5 2.3817 - 2.2110 1.00 3202 143 0.1507 0.1908
REMARK 3 6 2.2110 - 2.0807 1.00 3221 143 0.1503 0.1729
REMARK 3 7 2.0807 - 1.9765 1.00 3201 155 0.1506 0.1702
REMARK 3 8 1.9765 - 1.8905 1.00 3208 137 0.1632 0.2076
REMARK 3 9 1.8905 - 1.8177 1.00 3192 157 0.1656 0.2022
REMARK 3 10 1.8177 - 1.7550 1.00 3208 140 0.1640 0.1751
REMARK 3 11 1.7550 - 1.7001 1.00 3173 146 0.1833 0.2167
REMARK 3 12 1.7001 - 1.6515 1.00 3225 130 0.2013 0.2735
REMARK 3 13 1.6515 - 1.6080 0.99 3164 142 0.2160 0.2573
REMARK 3 14 1.6080 - 1.5688 0.95 3049 139 0.2351 0.2525
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) : 0.160
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.560
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 : 0.015 2482
REMARK 3 ANGLE : 1.208 3396
REMARK 3 CHIRALITY : 0.084 345
REMARK 3 PLANARITY : 0.009 440
REMARK 3 DIHEDRAL : 16.849 1440
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 12:354)
REMARK 3 ORIGIN FOR THE GROUP (A): -19.7510 12.6944 8.2741
REMARK 3 T TENSOR
REMARK 3 T11: 0.0963 T22: 0.1123
REMARK 3 T33: 0.1464 T12: -0.0138
REMARK 3 T13: -0.0153 T23: 0.0101
REMARK 3 L TENSOR
REMARK 3 L11: 0.3554 L22: 0.4693
REMARK 3 L33: 0.9758 L12: 0.0683
REMARK 3 L13: -0.0457 L23: 0.2833
REMARK 3 S TENSOR
REMARK 3 S11: -0.0410 S12: 0.0282 S13: -0.0255
REMARK 3 S21: 0.0741 S22: 0.0723 S23: -0.0320
REMARK 3 S31: -0.0202 S32: 0.1062 S33: 0.0082
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: (CHAIN A AND RESID 355:383)
REMARK 3 ORIGIN FOR THE GROUP (A): -26.3028 25.6479 24.0785
REMARK 3 T TENSOR
REMARK 3 T11: 0.2439 T22: 0.1254
REMARK 3 T33: 0.1068 T12: 0.0107
REMARK 3 T13: -0.0090 T23: -0.0136
REMARK 3 L TENSOR
REMARK 3 L11: 0.1244 L22: 0.1989
REMARK 3 L33: 0.1165 L12: 0.0010
REMARK 3 L13: 0.0483 L23: -0.0563
REMARK 3 S TENSOR
REMARK 3 S11: -0.0286 S12: -0.1479 S13: 0.1095
REMARK 3 S21: 0.3122 S22: 0.0391 S23: 0.0338
REMARK 3 S31: -0.2706 S32: -0.0153 S33: -0.0102
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: (CHAIN A AND RESID 384:427)
REMARK 3 ORIGIN FOR THE GROUP (A): -26.1830 20.5773 14.2978
REMARK 3 T TENSOR
REMARK 3 T11: 0.1613 T22: 0.0970
REMARK 3 T33: 0.1208 T12: -0.0017
REMARK 3 T13: 0.0181 T23: 0.0100
REMARK 3 L TENSOR
REMARK 3 L11: 0.2400 L22: 0.5328
REMARK 3 L33: 0.7093 L12: -0.0652
REMARK 3 L13: 0.2090 L23: 0.4744
REMARK 3 S TENSOR
REMARK 3 S11: -0.0836 S12: -0.0059 S13: 0.0818
REMARK 3 S21: 0.0482 S22: 0.0945 S23: -0.0238
REMARK 3 S31: -0.1320 S32: -0.0031 S33: 0.0110
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: (CHAIN A AND RESID 428:470)
REMARK 3 ORIGIN FOR THE GROUP (A): -4.8366 18.9291 3.9954
REMARK 3 T TENSOR
REMARK 3 T11: 0.1099 T22: 0.3185
REMARK 3 T33: 0.2158 T12: -0.0719
REMARK 3 T13: 0.0358 T23: -0.0347
REMARK 3 L TENSOR
REMARK 3 L11: 0.4802 L22: 1.1596
REMARK 3 L33: 0.5117 L12: -0.3258
REMARK 3 L13: 0.0843 L23: 0.3783
REMARK 3 S TENSOR
REMARK 3 S11: 0.1080 S12: -0.0344 S13: 0.0468
REMARK 3 S21: -0.1091 S22: 0.1017 S23: -0.2477
REMARK 3 S31: -0.2759 S32: 0.4108 S33: 0.2578
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: (CHAIN A AND RESID 471:588)
REMARK 3 ORIGIN FOR THE GROUP (A): -28.0516 14.3763 3.6944
REMARK 3 T TENSOR
REMARK 3 T11: 0.0933 T22: 0.0756
REMARK 3 T33: 0.0760 T12: -0.0109
REMARK 3 T13: -0.0009 T23: 0.0038
REMARK 3 L TENSOR
REMARK 3 L11: 0.5381 L22: 0.6721
REMARK 3 L33: 0.7705 L12: -0.3415
REMARK 3 L13: -0.0601 L23: 0.1848
REMARK 3 S TENSOR
REMARK 3 S11: 0.0183 S12: 0.0107 S13: -0.0525
REMARK 3 S21: 0.0390 S22: -0.0055 S23: 0.0660
REMARK 3 S31: -0.0277 S32: -0.0244 S33: 0.0522
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 5IVJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-16.
REMARK 100 THE DEPOSITION ID IS D_1000219500.
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 : 46861
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.569
REMARK 200 RESOLUTION RANGE LOW (A) : 32.979
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7
REMARK 200 DATA REDUNDANCY : 7.200
REMARK 200 R MERGE (I) : 0.12000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8
REMARK 200 DATA REDUNDANCY IN SHELL : 3.10
REMARK 200 R MERGE FOR SHELL (I) : 0.88500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
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 (%): 45.18
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 58.27800
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.25800
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.27800
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.25800
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 897 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 907 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 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 ARG A 349
REMARK 465 GLU A 350
REMARK 465 ALA A 351
REMARK 465 PHE A 352
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 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 ASP A 56 CG OD1 OD2
REMARK 470 GLU A 64 CG CD OE1 OE2
REMARK 470 LYS A 66 CG CD CE NZ
REMARK 470 GLU A 355 CG CD OE1 OE2
REMARK 470 GLN A 356 CG CD OE1 NE2
REMARK 470 VAL A 358 CG1 CG2
REMARK 470 ASP A 376 CG OD1 OD2
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 ARG A 428 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 430 CG CD CE NZ
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 LYS A 467 CG CD CE NZ
REMARK 470 ASP A 486 CG OD1 OD2
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: 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 882 O HOH A 929 2.05
REMARK 500 O HOH A 929 O HOH A 937 2.14
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 ALA A 357 89.24 -158.73
REMARK 500 PHE A 477 -6.25 80.50
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 99.0
REMARK 620 3 HIS A 571 NE2 83.7 85.4
REMARK 620 4 6ED A 601 N07 88.0 170.8 101.3
REMARK 620 5 HOH A 732 O 93.6 83.2 167.8 90.5
REMARK 620 6 HOH A 741 O 174.2 86.4 94.8 86.9 89.1
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 6ED 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 DMS A 604
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: 5IVE RELATED DB: PDB
REMARK 900 RELATED ID: 5IVF 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 5IVJ A 1 347 UNP P29375 KDM5A_HUMAN 1 87
DBREF 5IVJ A 348 588 UNP P29375 KDM5A_HUMAN 348 588
SEQADV 5IVJ HIS A -1 UNP P29375 EXPRESSION TAG
SEQADV 5IVJ 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 6ED A 601 40
HET MN A 602 1
HET GOL A 603 6
HET DMS A 604 4
HETNAM 6ED 3-({1-[2-(4,4-DIFLUOROPIPERIDIN-1-YL)ETHYL]-5-FLUORO-
HETNAM 2 6ED 1H-INDAZOL-3-YL}AMINO)PYRIDINE-4-CARBOXYLIC ACID
HETNAM MN MANGANESE (II) ION
HETNAM GOL GLYCEROL
HETNAM DMS DIMETHYL SULFOXIDE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 6ED C20 H20 F3 N5 O2
FORMUL 3 MN MN 2+
FORMUL 4 GOL C3 H8 O3
FORMUL 5 DMS C2 H6 O S
FORMUL 6 HOH *259(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 399 1 14
HELIX 6 AA6 SER A 415 GLY A 419 1 5
HELIX 7 AA7 LEU A 432 SER A 441 1 10
HELIX 8 AA8 ASN A 444 MET A 448 5 5
HELIX 9 AA9 GLU A 485 SER A 489 5 5
HELIX 10 AB1 PRO A 507 HIS A 509 5 3
HELIX 11 AB2 ALA A 510 ALA A 522 1 13
HELIX 12 AB3 PRO A 523 SER A 528 1 6
HELIX 13 AB4 PRO A 530 GLN A 535 1 6
HELIX 14 AB5 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 TYR A 472 O ALA A 581
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 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 GLN A 557 N LYS A 501
LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.26
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 N07 6ED A 601 MN MN A 602 1555 1555 2.27
LINK MN MN A 602 O HOH A 732 1555 1555 2.22
LINK MN MN A 602 O HOH A 741 1555 1555 2.19
SITE 1 AC1 19 ARG A 73 GLN A 75 TYR A 409 ALA A 411
SITE 2 AC1 19 ASP A 412 TRP A 470 TYR A 472 PHE A 480
SITE 3 AC1 19 HIS A 483 ASN A 493 LYS A 501 TRP A 503
SITE 4 AC1 19 GLN A 535 LEU A 536 HIS A 571 MN A 602
SITE 5 AC1 19 HOH A 741 HOH A 842 HOH A 920
SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 6ED A 601
SITE 2 AC2 6 HOH A 732 HOH A 741
SITE 1 AC3 7 MET A 380 PRO A 381 GLU A 485 HIS A 487
SITE 2 AC3 7 HOH A 711 HOH A 776 HOH A 781
SITE 1 AC4 2 GLY A 367 ASP A 371
CRYST1 116.556 62.516 46.772 90.00 92.32 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 0.008580 0.000000 0.000347 0.00000
SCALE2 0.000000 0.015996 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021398 0.00000