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 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 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