HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 21-MAR-16 5IW0
TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N19 [2-(5-((4-CHLORO-2-
TITLE 2 METHYLBENZYL)OXY)-1H-PYRAZOL-1-YL)ISONICOTINIC 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: ISTONE 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 5IW0 1 REMARK
REVDAT 2 03-AUG-16 5IW0 1 JRNL
REVDAT 1 27-JUL-16 5IW0 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. 1.63 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) : 1.63
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.97
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8
REMARK 3 NUMBER OF REFLECTIONS : 40578
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.159
REMARK 3 R VALUE (WORKING SET) : 0.157
REMARK 3 FREE R VALUE : 0.192
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980
REMARK 3 FREE R VALUE TEST SET COUNT : 2022
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 32.9763 - 3.9262 1.00 2906 160 0.1496 0.1753
REMARK 3 2 3.9262 - 3.1171 1.00 2859 151 0.1399 0.1616
REMARK 3 3 3.1171 - 2.7233 1.00 2877 141 0.1539 0.1963
REMARK 3 4 2.7233 - 2.4744 1.00 2836 159 0.1570 0.1925
REMARK 3 5 2.4744 - 2.2971 1.00 2847 143 0.1574 0.1929
REMARK 3 6 2.2971 - 2.1617 1.00 2833 140 0.1490 0.1829
REMARK 3 7 2.1617 - 2.0535 1.00 2845 154 0.1491 0.1822
REMARK 3 8 2.0535 - 1.9641 1.00 2851 153 0.1504 0.1953
REMARK 3 9 1.9641 - 1.8885 1.00 2828 151 0.1699 0.2376
REMARK 3 10 1.8885 - 1.8233 1.00 2830 149 0.1720 0.2209
REMARK 3 11 1.8233 - 1.7663 1.00 2834 147 0.1789 0.2174
REMARK 3 12 1.7663 - 1.7158 0.99 2815 142 0.2092 0.2698
REMARK 3 13 1.7158 - 1.6707 0.92 2587 134 0.2274 0.2555
REMARK 3 14 1.6707 - 1.6299 0.65 1808 98 0.2478 0.2945
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) : 19.410
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 : 0.005 2564
REMARK 3 ANGLE : 0.732 3505
REMARK 3 CHIRALITY : 0.049 360
REMARK 3 PLANARITY : 0.006 463
REMARK 3 DIHEDRAL : 16.844 1475
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 12 THROUGH 31 )
REMARK 3 ORIGIN FOR THE GROUP (A): -17.5412 2.4541 8.4974
REMARK 3 T TENSOR
REMARK 3 T11: 0.1268 T22: 0.1789
REMARK 3 T33: 0.2685 T12: 0.0426
REMARK 3 T13: -0.0127 T23: -0.0281
REMARK 3 L TENSOR
REMARK 3 L11: 0.0338 L22: 0.0431
REMARK 3 L33: 0.1327 L12: 0.0341
REMARK 3 L13: 0.0688 L23: 0.0697
REMARK 3 S TENSOR
REMARK 3 S11: 0.1475 S12: -0.0071 S13: -0.0336
REMARK 3 S21: 0.1742 S22: 0.0901 S23: -0.1693
REMARK 3 S31: 0.2347 S32: 0.1127 S33: 0.0365
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 81 )
REMARK 3 ORIGIN FOR THE GROUP (A): -18.3922 14.6853 8.0734
REMARK 3 T TENSOR
REMARK 3 T11: 0.1632 T22: 0.1422
REMARK 3 T33: 0.1794 T12: -0.0094
REMARK 3 T13: -0.0187 T23: -0.0037
REMARK 3 L TENSOR
REMARK 3 L11: 0.1686 L22: 0.1323
REMARK 3 L33: 0.2450 L12: 0.1058
REMARK 3 L13: -0.0957 L23: -0.0387
REMARK 3 S TENSOR
REMARK 3 S11: 0.0044 S12: 0.0240 S13: 0.0021
REMARK 3 S21: -0.0324 S22: 0.0163 S23: 0.0055
REMARK 3 S31: -0.1151 S32: 0.0368 S33: -0.0000
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 82 THROUGH 362 )
REMARK 3 ORIGIN FOR THE GROUP (A): -35.0714 35.2414 13.9597
REMARK 3 T TENSOR
REMARK 3 T11: 0.4149 T22: 0.1918
REMARK 3 T33: 0.2381 T12: 0.0327
REMARK 3 T13: -0.0627 T23: 0.0078
REMARK 3 L TENSOR
REMARK 3 L11: 0.0127 L22: -0.0011
REMARK 3 L33: 0.0162 L12: 0.0044
REMARK 3 L13: -0.0141 L23: -0.0095
REMARK 3 S TENSOR
REMARK 3 S11: 0.0625 S12: 0.0644 S13: 0.0484
REMARK 3 S21: -0.0186 S22: 0.1433 S23: -0.0211
REMARK 3 S31: -0.0545 S32: -0.1379 S33: 0.0011
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 363 THROUGH 405 )
REMARK 3 ORIGIN FOR THE GROUP (A): -31.5010 18.9534 22.4612
REMARK 3 T TENSOR
REMARK 3 T11: 0.2188 T22: 0.1883
REMARK 3 T33: 0.1385 T12: 0.0242
REMARK 3 T13: 0.0236 T23: 0.0053
REMARK 3 L TENSOR
REMARK 3 L11: 0.0660 L22: 0.0852
REMARK 3 L33: 0.1444 L12: -0.0347
REMARK 3 L13: -0.0928 L23: 0.0120
REMARK 3 S TENSOR
REMARK 3 S11: -0.0537 S12: -0.1424 S13: 0.0022
REMARK 3 S21: 0.3144 S22: 0.0610 S23: 0.0774
REMARK 3 S31: -0.0423 S32: -0.1354 S33: 0.0000
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 432 )
REMARK 3 ORIGIN FOR THE GROUP (A): -11.4232 26.4619 9.9911
REMARK 3 T TENSOR
REMARK 3 T11: 0.1803 T22: 0.2087
REMARK 3 T33: 0.2095 T12: -0.0599
REMARK 3 T13: 0.0170 T23: -0.0256
REMARK 3 L TENSOR
REMARK 3 L11: 0.0386 L22: 0.0105
REMARK 3 L33: 0.0266 L12: 0.0062
REMARK 3 L13: -0.0172 L23: 0.0293
REMARK 3 S TENSOR
REMARK 3 S11: -0.0227 S12: 0.0463 S13: 0.2585
REMARK 3 S21: 0.0763 S22: 0.0932 S23: -0.0735
REMARK 3 S31: -0.2818 S32: 0.1719 S33: 0.0106
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 459 )
REMARK 3 ORIGIN FOR THE GROUP (A): -5.4764 17.5050 -1.4605
REMARK 3 T TENSOR
REMARK 3 T11: -0.0129 T22: 0.2511
REMARK 3 T33: 0.1450 T12: -0.0541
REMARK 3 T13: 0.0146 T23: -0.0144
REMARK 3 L TENSOR
REMARK 3 L11: 0.3865 L22: 0.2819
REMARK 3 L33: 0.2142 L12: -0.1648
REMARK 3 L13: -0.0481 L23: 0.1126
REMARK 3 S TENSOR
REMARK 3 S11: 0.1190 S12: 0.0398 S13: 0.0344
REMARK 3 S21: -0.2281 S22: -0.0409 S23: -0.0676
REMARK 3 S31: -0.0631 S32: 0.2011 S33: 0.0972
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 460 THROUGH 588 )
REMARK 3 ORIGIN FOR THE GROUP (A): -27.2784 14.8751 3.5726
REMARK 3 T TENSOR
REMARK 3 T11: 0.0798 T22: 0.0547
REMARK 3 T33: 0.0633 T12: -0.0044
REMARK 3 T13: -0.0022 T23: 0.0055
REMARK 3 L TENSOR
REMARK 3 L11: 0.2538 L22: 0.3291
REMARK 3 L33: 0.3979 L12: -0.1287
REMARK 3 L13: 0.0723 L23: 0.0152
REMARK 3 S TENSOR
REMARK 3 S11: 0.0122 S12: 0.0094 S13: -0.0326
REMARK 3 S21: -0.0072 S22: 0.0082 S23: 0.0446
REMARK 3 S31: -0.0303 S32: -0.0072 S33: 0.0651
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 5IW0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-16.
REMARK 100 THE DEPOSITION ID IS D_1000219529.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-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 : 40597
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630
REMARK 200 RESOLUTION RANGE LOW (A) : 32.970
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4
REMARK 200 DATA REDUNDANCY : 6.200
REMARK 200 R MERGE (I) : 0.11200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.3000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.63000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800
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 (%): 45.09
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 58.16000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.37050
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.16000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.37050
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 883 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 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 GLU A 81 CG CD OE1 OE2
REMARK 470 ARG A 349 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 350 CG CD OE1 OE2
REMARK 470 GLU A 355 CG CD OE1 OE2
REMARK 470 VAL A 358 CG1 CG2
REMARK 470 ARG A 359 CG CD NE CZ NH1 NH2
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 LYS A 430 CG CD CE NZ
REMARK 470 GLU A 452 CG CD OE1 OE2
REMARK 470 ASN A 460 CG OD1 ND2
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 811 O HOH A 885 2.16
REMARK 500 O4 AKG A 602 O HOH A 701 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 PHE A 477 -7.71 80.23
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 603 MN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 HIS A 483 NE2
REMARK 620 2 GLU A 485 OE1 97.4
REMARK 620 3 HIS A 571 NE2 83.4 89.3
REMARK 620 4 6EP A 601 N08 82.8 100.2 164.1
REMARK 620 5 6EP A 601 N22 92.1 168.4 98.4 74.3
REMARK 620 6 HOH A 776 O 174.9 87.7 96.8 96.3 82.8
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 6EP A 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 604
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO 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 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: 5IVJ RELATED DB: PDB
REMARK 900 RELATED ID: 5IVV RELATED DB: PDB
REMARK 900 RELATED ID: 5IVY RELATED DB: PDB
REMARK 900 RELATED ID: 5IWF RELATED DB: PDB
DBREF 5IW0 A 1 347 UNP P29375 KDM5A_HUMAN 1 87
DBREF 5IW0 A 348 588 UNP P29375 KDM5A_HUMAN 348 588
SEQADV 5IW0 HIS A -1 UNP P29375 EXPRESSION TAG
SEQADV 5IW0 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 6EP A 601 24
HET AKG A 602 20
HET MN A 603 1
HET EDO A 604 4
HET EDO A 605 4
HET GOL A 606 6
HET GOL A 607 6
HETNAM 6EP 2-{5-[(4-CHLORO-2-METHYLPHENYL)METHOXY]-1H-PYRAZOL-1-
HETNAM 2 6EP YL}PYRIDINE-4-CARBOXYLIC ACID
HETNAM AKG 2-OXOGLUTARIC ACID
HETNAM MN MANGANESE (II) ION
HETNAM EDO 1,2-ETHANEDIOL
HETNAM GOL GLYCEROL
HETSYN EDO ETHYLENE GLYCOL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 6EP C17 H14 CL N3 O3
FORMUL 3 AKG C5 H6 O5
FORMUL 4 MN MN 2+
FORMUL 5 EDO 2(C2 H6 O2)
FORMUL 7 GOL 2(C3 H8 O3)
FORMUL 9 HOH *218(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 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 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 ASN A 493 O VAL A 563
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 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 603 1555 1555 2.27
LINK OE1 GLU A 485 MN MN A 603 1555 1555 2.07
LINK NE2 HIS A 571 MN MN A 603 1555 1555 2.29
LINK N08 6EP A 601 MN MN A 603 1555 1555 2.26
LINK N22 6EP A 601 MN MN A 603 1555 1555 2.27
LINK MN MN A 603 O HOH A 776 1555 1555 2.17
SITE 1 AC1 15 ARG A 73 GLN A 75 TYR A 409 ALA A 411
SITE 2 AC1 15 ASP A 412 TYR A 472 PHE A 480 HIS A 483
SITE 3 AC1 15 GLU A 485 LYS A 501 TRP A 503 HIS A 571
SITE 4 AC1 15 AKG A 602 MN A 603 HOH A 776
SITE 1 AC2 9 LYS A 45 SER A 479 PHE A 480 CYS A 481
SITE 2 AC2 9 HIS A 483 GLN A 535 LEU A 536 6EP A 601
SITE 3 AC2 9 HOH A 701
SITE 1 AC3 5 HIS A 483 GLU A 485 HIS A 571 6EP A 601
SITE 2 AC3 5 HOH A 776
SITE 1 AC4 4 GLU A 64 VAL A 65 LYS A 66 ARG A 429
SITE 1 AC5 5 ILE A 539 MET A 540 ASN A 541 HOH A 710
SITE 2 AC5 5 HOH A 765
SITE 1 AC6 8 SER A 375 ASN A 379 MET A 380 PRO A 381
SITE 2 AC6 8 ASP A 486 HIS A 487 HOH A 715 HOH A 802
SITE 1 AC7 9 LYS A 45 GLN A 75 ARG A 76 LEU A 77
SITE 2 AC7 9 GLU A 79 SER A 479 HOH A 701 HOH A 745
SITE 3 AC7 9 HOH A 848
CRYST1 116.320 62.741 46.609 90.00 91.93 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 0.008597 0.000000 0.000290 0.00000
SCALE2 0.000000 0.015939 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021467 0.00000