HEADER OXIDOREDUCTASE/INHIBITOR 29-OCT-17 6BGV
TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-CHLOROPHENYL)(2-
TITLE 2 (PIPERIDIN-1-YL)ETHOXY)METHYL)-1L2-PYRROLO[3,2-B]PYRIDINE-7-
TITLE 3 CARBOXYLIC ACID (COMPOUND N40)
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 6BGV 1 LINK
REVDAT 3 01-JAN-20 6BGV 1 REMARK
REVDAT 2 25-APR-18 6BGV 1 JRNL
REVDAT 1 28-MAR-18 6BGV 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. 1.59 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 : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.94
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 43547
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.169
REMARK 3 R VALUE (WORKING SET) : 0.168
REMARK 3 FREE R VALUE : 0.184
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.620
REMARK 3 FREE R VALUE TEST SET COUNT : 2014
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 30.9473 - 3.8353 1.00 3091 156 0.1576 0.1493
REMARK 3 2 3.8353 - 3.0450 1.00 3053 144 0.1514 0.1836
REMARK 3 3 3.0450 - 2.6603 0.99 3016 141 0.1705 0.1835
REMARK 3 4 2.6603 - 2.4172 0.99 3007 145 0.1767 0.1949
REMARK 3 5 2.4172 - 2.2440 0.99 3001 139 0.1605 0.1754
REMARK 3 6 2.2440 - 2.1117 0.99 2988 150 0.1609 0.2049
REMARK 3 7 2.1117 - 2.0060 0.99 2968 143 0.1649 0.1751
REMARK 3 8 2.0060 - 1.9187 0.98 3005 142 0.1706 0.2071
REMARK 3 9 1.9187 - 1.8448 0.98 2930 150 0.1704 0.1835
REMARK 3 10 1.8448 - 1.7812 0.98 2958 142 0.1753 0.1864
REMARK 3 11 1.7812 - 1.7255 0.98 2932 145 0.1939 0.2205
REMARK 3 12 1.7255 - 1.6762 0.98 2958 139 0.1974 0.2206
REMARK 3 13 1.6762 - 1.6321 0.97 2946 134 0.2144 0.2376
REMARK 3 14 1.6321 - 1.5922 0.90 2680 144 0.2215 0.2459
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
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) : 0.150
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.600
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 2606
REMARK 3 ANGLE : 0.554 3555
REMARK 3 CHIRALITY : 0.046 366
REMARK 3 PLANARITY : 0.005 461
REMARK 3 DIHEDRAL : 10.575 1496
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 11
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 31 )
REMARK 3 ORIGIN FOR THE GROUP (A): -18.2522 2.6876 8.6108
REMARK 3 T TENSOR
REMARK 3 T11: 0.1555 T22: 0.1207
REMARK 3 T33: 0.1813 T12: 0.0226
REMARK 3 T13: -0.0187 T23: 0.0014
REMARK 3 L TENSOR
REMARK 3 L11: 5.2720 L22: 1.5932
REMARK 3 L33: 1.3619 L12: -0.0720
REMARK 3 L13: -0.2114 L23: 0.2693
REMARK 3 S TENSOR
REMARK 3 S11: -0.0532 S12: -0.0486 S13: -0.0051
REMARK 3 S21: 0.1615 S22: 0.0960 S23: -0.2808
REMARK 3 S31: 0.2014 S32: 0.2152 S33: -0.0496
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 46 )
REMARK 3 ORIGIN FOR THE GROUP (A): -15.6137 1.9371 -2.1845
REMARK 3 T TENSOR
REMARK 3 T11: 0.1517 T22: 0.1415
REMARK 3 T33: 0.1703 T12: -0.0059
REMARK 3 T13: -0.0023 T23: -0.0119
REMARK 3 L TENSOR
REMARK 3 L11: 7.2436 L22: 2.4537
REMARK 3 L33: 1.7107 L12: 2.8193
REMARK 3 L13: -0.6480 L23: 0.1906
REMARK 3 S TENSOR
REMARK 3 S11: 0.1049 S12: 0.3301 S13: -0.1543
REMARK 3 S21: -0.1742 S22: 0.0394 S23: -0.1792
REMARK 3 S31: -0.0584 S32: 0.1463 S33: -0.1017
REMARK 3 TLS GROUP : 3
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 47 THROUGH 76 )
REMARK 3 ORIGIN FOR THE GROUP (A): -14.8662 19.5242 12.5575
REMARK 3 T TENSOR
REMARK 3 T11: 0.1581 T22: 0.1603
REMARK 3 T33: 0.1446 T12: -0.0309
REMARK 3 T13: -0.0273 T23: 0.0168
REMARK 3 L TENSOR
REMARK 3 L11: 1.2809 L22: 1.7208
REMARK 3 L33: 0.6059 L12: -0.4702
REMARK 3 L13: -0.1436 L23: 0.3803
REMARK 3 S TENSOR
REMARK 3 S11: 0.0256 S12: -0.1153 S13: 0.1061
REMARK 3 S21: 0.0539 S22: 0.0241 S23: -0.3123
REMARK 3 S31: -0.1106 S32: 0.1259 S33: -0.0415
REMARK 3 TLS GROUP : 4
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 359 )
REMARK 3 ORIGIN FOR THE GROUP (A): -41.1043 31.0426 11.3888
REMARK 3 T TENSOR
REMARK 3 T11: 0.3649 T22: 0.3257
REMARK 3 T33: 0.4577 T12: 0.0526
REMARK 3 T13: -0.0388 T23: -0.0364
REMARK 3 L TENSOR
REMARK 3 L11: 0.6945 L22: 2.2306
REMARK 3 L33: 0.8242 L12: -0.4850
REMARK 3 L13: -0.5465 L23: -0.2460
REMARK 3 S TENSOR
REMARK 3 S11: -0.0215 S12: -0.1207 S13: 0.8046
REMARK 3 S21: -0.1932 S22: -0.1979 S23: 0.2271
REMARK 3 S31: -0.6217 S32: -0.2297 S33: 0.1164
REMARK 3 TLS GROUP : 5
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 378 )
REMARK 3 ORIGIN FOR THE GROUP (A): -25.3612 26.0314 23.7078
REMARK 3 T TENSOR
REMARK 3 T11: 0.2336 T22: 0.1344
REMARK 3 T33: 0.1022 T12: 0.0195
REMARK 3 T13: -0.0143 T23: -0.0212
REMARK 3 L TENSOR
REMARK 3 L11: 3.4366 L22: 4.2046
REMARK 3 L33: 2.1544 L12: 2.3112
REMARK 3 L13: -0.9142 L23: -1.3084
REMARK 3 S TENSOR
REMARK 3 S11: 0.0139 S12: -0.3082 S13: 0.0969
REMARK 3 S21: 0.4754 S22: -0.0488 S23: -0.0801
REMARK 3 S31: -0.2812 S32: 0.0469 S33: 0.0165
REMARK 3 TLS GROUP : 6
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 379 THROUGH 405 )
REMARK 3 ORIGIN FOR THE GROUP (A): -35.4209 15.4511 20.7839
REMARK 3 T TENSOR
REMARK 3 T11: 0.1757 T22: 0.1724
REMARK 3 T33: 0.1411 T12: -0.0079
REMARK 3 T13: 0.0624 T23: -0.0014
REMARK 3 L TENSOR
REMARK 3 L11: 0.5402 L22: 1.4462
REMARK 3 L33: 2.8548 L12: 0.8564
REMARK 3 L13: 0.5790 L23: 0.6726
REMARK 3 S TENSOR
REMARK 3 S11: -0.0026 S12: -0.1736 S13: 0.0609
REMARK 3 S21: 0.2345 S22: -0.0998 S23: 0.1212
REMARK 3 S31: 0.2500 S32: -0.3679 S33: 0.0743
REMARK 3 TLS GROUP : 7
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 440 )
REMARK 3 ORIGIN FOR THE GROUP (A): -7.5900 24.0449 10.2087
REMARK 3 T TENSOR
REMARK 3 T11: 0.1784 T22: 0.2764
REMARK 3 T33: 0.2561 T12: -0.0441
REMARK 3 T13: 0.0001 T23: -0.0343
REMARK 3 L TENSOR
REMARK 3 L11: 2.9135 L22: 0.7926
REMARK 3 L33: 0.2879 L12: -0.7896
REMARK 3 L13: -0.3041 L23: 0.3375
REMARK 3 S TENSOR
REMARK 3 S11: -0.0985 S12: -0.1025 S13: 0.4948
REMARK 3 S21: 0.0931 S22: 0.1898 S23: -0.3727
REMARK 3 S31: -0.1556 S32: 0.3198 S33: -0.0844
REMARK 3 TLS GROUP : 8
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 441 THROUGH 485 )
REMARK 3 ORIGIN FOR THE GROUP (A): -16.8736 19.7538 -0.4741
REMARK 3 T TENSOR
REMARK 3 T11: 0.1410 T22: 0.1507
REMARK 3 T33: 0.1155 T12: -0.0221
REMARK 3 T13: 0.0226 T23: 0.0266
REMARK 3 L TENSOR
REMARK 3 L11: 1.0432 L22: 1.2017
REMARK 3 L33: 0.7176 L12: -0.3553
REMARK 3 L13: 0.6323 L23: 0.3391
REMARK 3 S TENSOR
REMARK 3 S11: 0.0484 S12: 0.2544 S13: 0.0485
REMARK 3 S21: -0.1425 S22: -0.0241 S23: -0.1572
REMARK 3 S31: -0.1699 S32: 0.2108 S33: -0.0336
REMARK 3 TLS GROUP : 9
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 486 THROUGH 507 )
REMARK 3 ORIGIN FOR THE GROUP (A): -20.9336 13.9772 5.5467
REMARK 3 T TENSOR
REMARK 3 T11: 0.1064 T22: 0.0721
REMARK 3 T33: 0.0969 T12: -0.0020
REMARK 3 T13: 0.0011 T23: 0.0158
REMARK 3 L TENSOR
REMARK 3 L11: 1.1772 L22: 0.4142
REMARK 3 L33: 1.6643 L12: 0.2579
REMARK 3 L13: 0.5362 L23: 0.8056
REMARK 3 S TENSOR
REMARK 3 S11: -0.0363 S12: 0.0184 S13: 0.0328
REMARK 3 S21: 0.0040 S22: -0.0034 S23: -0.0099
REMARK 3 S31: -0.0841 S32: 0.0721 S33: 0.0553
REMARK 3 TLS GROUP : 10
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 541 )
REMARK 3 ORIGIN FOR THE GROUP (A): -38.0834 16.4443 -3.2548
REMARK 3 T TENSOR
REMARK 3 T11: 0.2106 T22: 0.2215
REMARK 3 T33: 0.2267 T12: 0.0192
REMARK 3 T13: -0.0018 T23: -0.0221
REMARK 3 L TENSOR
REMARK 3 L11: 0.6964 L22: 1.2453
REMARK 3 L33: 0.2392 L12: -0.7048
REMARK 3 L13: 0.0762 L23: -0.4956
REMARK 3 S TENSOR
REMARK 3 S11: 0.0726 S12: 0.1834 S13: -0.0573
REMARK 3 S21: -0.1053 S22: -0.1162 S23: 0.2977
REMARK 3 S31: -0.1012 S32: -0.1912 S33: 0.0354
REMARK 3 TLS GROUP : 11
REMARK 3 SELECTION: CHAIN 'A' AND (RESID 542 THROUGH 588 )
REMARK 3 ORIGIN FOR THE GROUP (A): -24.9050 11.3549 5.6883
REMARK 3 T TENSOR
REMARK 3 T11: 0.0944 T22: 0.0760
REMARK 3 T33: 0.0916 T12: 0.0012
REMARK 3 T13: 0.0074 T23: 0.0114
REMARK 3 L TENSOR
REMARK 3 L11: 0.9799 L22: 1.2476
REMARK 3 L33: 1.5323 L12: 0.1152
REMARK 3 L13: 0.2046 L23: 0.6222
REMARK 3 S TENSOR
REMARK 3 S11: 0.0083 S12: 0.0100 S13: -0.0629
REMARK 3 S21: 0.0196 S22: -0.0116 S23: 0.0084
REMARK 3 S31: 0.0177 S32: -0.0420 S33: 0.0031
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 6BGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-17.
REMARK 100 THE DEPOSITION ID IS D_1000230642.
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) : 1.000000
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 : 43550
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590
REMARK 200 RESOLUTION RANGE LOW (A) : 30.942
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4
REMARK 200 DATA REDUNDANCY : 6.800
REMARK 200 R MERGE (I) : 0.15500
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.65
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.74300
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200
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 (%): 44.45
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21
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 58.14450
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.94150
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.14450
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.94150
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 910 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 915 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 ASP A 56 CG OD1 OD2
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 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 GLU A 355 CG CD OE1 OE2
REMARK 470 ARG A 359 CG CD NE CZ NH1 NH2
REMARK 470 GLU A 368 CG CD OE1 OE2
REMARK 470 LYS A 392 CG CD CE NZ
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 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 -9.54 80.27
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 96.8
REMARK 620 3 HIS A 571 NE2 83.7 85.5
REMARK 620 4 DQG A 601 N28 88.3 172.0 101.2
REMARK 620 5 HOH A 753 O 96.9 80.7 166.2 92.6
REMARK 620 6 HOH A 872 O 173.4 89.7 96.1 85.3 84.9
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 DQG 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 DMS 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
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 609
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 610
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 611
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 612
DBREF 6BGV A 1 347 UNP P29375 KDM5A_HUMAN 1 87
DBREF 6BGV A 348 588 UNP P29375 KDM5A_HUMAN 348 588
SEQADV 6BGV HIS A -1 UNP P29375 EXPRESSION TAG
SEQADV 6BGV 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 DQG A 601 37
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 DMS A 607 4
HET DMS A 608 4
HET EDO A 609 4
HET EDO A 610 4
HET EDO A 611 4
HET EDO A 612 4
HETNAM DQG 2-{(S)-(2-CHLOROPHENYL)[2-(PIPERIDIN-1-YL)
HETNAM 2 DQG ETHOXY]METHYL}-1H-PYRROLO[3,2-B]PYRIDINE-7-CARBOXYLIC
HETNAM 3 DQG ACID
HETNAM MN MANGANESE (II) ION
HETNAM GOL GLYCEROL
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 DQG C22 H24 CL N3 O3
FORMUL 3 MN MN 2+
FORMUL 4 GOL 4(C3 H8 O3)
FORMUL 8 DMS 2(C2 H6 O S)
FORMUL 10 EDO 4(C2 H6 O2)
FORMUL 14 HOH *242(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 LEU A 440 1 6
HELIX 9 AA9 ASN A 444 MET A 448 5 5
HELIX 10 AB1 VAL A 455 ASN A 460 1 6
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 2.25
LINK OE2 GLU A 485 MN MN A 602 1555 1555 2.06
LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.30
LINK N28 DQG A 601 MN MN A 602 1555 1555 2.33
LINK MN MN A 602 O HOH A 753 1555 1555 2.23
LINK MN MN A 602 O HOH A 872 1555 1555 2.11
SITE 1 AC1 17 ARG A 73 TYR A 409 ALA A 411 ASP A 412
SITE 2 AC1 17 TRP A 470 TYR A 472 SER A 479 PHE A 480
SITE 3 AC1 17 CYS A 481 HIS A 483 LYS A 501 TRP A 503
SITE 4 AC1 17 HIS A 571 MN A 602 EDO A 609 HOH A 870
SITE 5 AC1 17 HOH A 872
SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 DQG A 601
SITE 2 AC2 6 HOH A 753 HOH A 872
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 707 HOH A 778
SITE 3 AC3 9 HOH A 830
SITE 1 AC4 8 GLU A 81 SER A 399 ILE A 539 MET A 540
SITE 2 AC4 8 ASN A 541 HOH A 721 HOH A 760 HOH A 856
SITE 1 AC5 8 GLU A 515 MET A 518 ASP A 531 HIS A 534
SITE 2 AC5 8 GLN A 535 TYR A 570 HOH A 706 HOH A 726
SITE 1 AC6 7 ARG A 40 ARG A 76 GLU A 79 HOH A 823
SITE 2 AC6 7 HOH A 852 HOH A 857 HOH A 881
SITE 1 AC7 1 TRP A 497
SITE 1 AC8 5 CYS A 63 GLU A 64 VAL A 65 LYS A 66
SITE 2 AC8 5 ARG A 429
SITE 1 AC9 6 LYS A 45 ARG A 73 HIS A 509 LEU A 536
SITE 2 AC9 6 TYR A 553 DQG A 601
SITE 1 AD1 2 PRO A 53 HOH A 771
SITE 1 AD2 3 ARG A 69 GLU A 512 HOH A 703
SITE 1 AD3 7 SER A 479 PHE A 480 CYS A 481 ILE A 539
SITE 2 AD3 7 HOH A 717 HOH A 862 HOH A 890
CRYST1 116.289 61.883 46.735 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 0.008599 0.000000 0.000349 0.00000
SCALE2 0.000000 0.016160 0.000000 0.00000
SCALE3 0.000000 0.000000 0.021415 0.00000