HEADER OXIDOREDUCTASE/INHIBITOR 10-JUN-18 6DQ7 TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE POTENTIAL HYDROLYSIS PRODUCT OF TITLE 2 INHIBITOR N45 I.E. 3-((6-(4-(2-CYANO-3-METHYLBUT-2-ENOYL)-1,4- TITLE 3 DIAZEPAN-1-YL)-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL)AMINO)PROPANOIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: 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-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 11-OCT-23 6DQ7 1 REMARK REVDAT 2 01-JAN-20 6DQ7 1 REMARK REVDAT 1 12-JUN-19 6DQ7 0 JRNL AUTH J.R.HORTON,X.LIU,C.B.WOODCOCK,J.SHANKS,X.ZHANG,G.RAI,B.MOTT, JRNL AUTH 2 D.J.JANSEN,S.KALES,M.J.HENDERSON,K.POHIDA,Y.FANG,X.HU, JRNL AUTH 3 A.JADHAV,D.MALONEY,M.D.HALL,A.SIMEONOV,H.FU,P.M.VERTINO, JRNL AUTH 4 X.CHENG JRNL TITL STRUCTURE-BASED ENGINEERING OF REVERSIBLE COVALENT JRNL TITL 2 INHIBITORS AGAINST HISTONE LYSINE DEMETHYLASE 5A JRNL REF TO BE PUBLISHED JRNL REFN 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 1 REFERENCE 3 REMARK 1 AUTH J.R.HORTON,X.LIU,L.WU,K.ZHANG,J.SHANKS,X.ZHANG,G.RAI, REMARK 1 AUTH 2 B.T.MOTT,D.J.JANSEN,S.C.KALES,M.J.HENDERSON,K.POHIDA,Y.FANG, REMARK 1 AUTH 3 X.HU,A.JADHAV,D.J.MALONEY,M.D.HALL,A.SIMEONOV,H.FU, REMARK 1 AUTH 4 P.M.VERTINO,Q.YAN,X.CHENG REMARK 1 TITL INSIGHTS INTO THE ACTION OF INHIBITOR ENANTIOMERS AGAINST REMARK 1 TITL 2 HISTONE LYSINE DEMETHYLASE 5A. REMARK 1 REF J. MED. CHEM. V. 61 3193 2018 REMARK 1 REFN ISSN 1520-4804 REMARK 1 PMID 29537847 REMARK 1 DOI 10.1021/ACS.JMEDCHEM.8B00261 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (DEV_2666: ???) 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 28572 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1425 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 33.1455 - 3.9882 1.00 2800 152 0.1677 0.1579 REMARK 3 2 3.9882 - 3.1663 1.00 2747 135 0.1669 0.1980 REMARK 3 3 3.1663 - 2.7663 1.00 2736 152 0.1914 0.2130 REMARK 3 4 2.7663 - 2.5135 1.00 2735 150 0.2062 0.2508 REMARK 3 5 2.5135 - 2.3334 1.00 2728 129 0.2054 0.2585 REMARK 3 6 2.3334 - 2.1958 1.00 2746 145 0.2052 0.2075 REMARK 3 7 2.1958 - 2.0859 1.00 2708 136 0.2116 0.2404 REMARK 3 8 2.0859 - 1.9951 1.00 2722 152 0.2119 0.2417 REMARK 3 9 1.9951 - 1.9183 1.00 2705 138 0.2434 0.2528 REMARK 3 10 1.9183 - 1.8521 0.93 2520 136 0.2968 0.3558 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.320 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 : NULL NULL REMARK 3 ANGLE : 0.465 3375 REMARK 3 CHIRALITY : 0.042 345 REMARK 3 PLANARITY : 0.004 442 REMARK 3 DIHEDRAL : 4.901 1953 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): -19.0987 2.5153 9.0022 REMARK 3 T TENSOR REMARK 3 T11: 0.2702 T22: 0.1869 REMARK 3 T33: 0.2261 T12: 0.0138 REMARK 3 T13: -0.0145 T23: -0.0018 REMARK 3 L TENSOR REMARK 3 L11: 6.3153 L22: 3.5002 REMARK 3 L33: 2.5929 L12: -0.8783 REMARK 3 L13: 0.7456 L23: 0.7974 REMARK 3 S TENSOR REMARK 3 S11: -0.3575 S12: -0.0969 S13: -0.2464 REMARK 3 S21: 0.1851 S22: 0.3196 S23: -0.3530 REMARK 3 S31: 0.1779 S32: 0.3245 S33: 0.0195 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.8498 6.7528 5.6953 REMARK 3 T TENSOR REMARK 3 T11: 0.2053 T22: 0.2296 REMARK 3 T33: 0.2233 T12: 0.0159 REMARK 3 T13: -0.0270 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 2.1120 L22: 3.3271 REMARK 3 L33: 1.6855 L12: 1.1596 REMARK 3 L13: -0.0930 L23: 1.0073 REMARK 3 S TENSOR REMARK 3 S11: 0.0249 S12: 0.0240 S13: -0.2306 REMARK 3 S21: 0.0815 S22: 0.0814 S23: -0.3328 REMARK 3 S31: 0.1343 S32: 0.3065 S33: -0.0943 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 359 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.6820 28.7175 12.1852 REMARK 3 T TENSOR REMARK 3 T11: 0.3645 T22: 0.2280 REMARK 3 T33: 0.2950 T12: 0.0557 REMARK 3 T13: 0.0248 T23: 0.0246 REMARK 3 L TENSOR REMARK 3 L11: 2.4096 L22: 4.3359 REMARK 3 L33: 2.0140 L12: 3.1947 REMARK 3 L13: 0.3208 L23: 0.4914 REMARK 3 S TENSOR REMARK 3 S11: -0.1218 S12: 0.4215 S13: 0.6471 REMARK 3 S21: -0.0138 S22: 0.2076 S23: 0.3805 REMARK 3 S31: -0.3290 S32: -0.1368 S33: -0.0217 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 360 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.3418 25.9334 23.6934 REMARK 3 T TENSOR REMARK 3 T11: 0.3135 T22: 0.2084 REMARK 3 T33: 0.2000 T12: 0.0194 REMARK 3 T13: -0.0153 T23: -0.0391 REMARK 3 L TENSOR REMARK 3 L11: 5.0574 L22: 6.0320 REMARK 3 L33: 3.9174 L12: 3.0859 REMARK 3 L13: -1.7263 L23: -2.0958 REMARK 3 S TENSOR REMARK 3 S11: 0.1686 S12: -0.2277 S13: 0.2224 REMARK 3 S21: 0.7148 S22: -0.0944 S23: -0.0429 REMARK 3 S31: -0.6114 S32: 0.0439 S33: -0.1013 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 379 THROUGH 399 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.9557 13.3989 21.7490 REMARK 3 T TENSOR REMARK 3 T11: 0.2630 T22: 0.2315 REMARK 3 T33: 0.1844 T12: -0.0006 REMARK 3 T13: 0.0513 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.8355 L22: 1.8146 REMARK 3 L33: 4.1984 L12: 0.6800 REMARK 3 L13: 0.9688 L23: 0.5668 REMARK 3 S TENSOR REMARK 3 S11: 0.1198 S12: -0.0991 S13: -0.0889 REMARK 3 S21: 0.2632 S22: -0.0220 S23: 0.0087 REMARK 3 S31: 0.5176 S32: -0.2149 S33: -0.0525 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 400 THROUGH 432 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.8002 25.5770 11.5191 REMARK 3 T TENSOR REMARK 3 T11: 0.2971 T22: 0.2263 REMARK 3 T33: 0.3394 T12: -0.0794 REMARK 3 T13: 0.0195 T23: -0.0541 REMARK 3 L TENSOR REMARK 3 L11: 1.9096 L22: 1.4826 REMARK 3 L33: 1.9862 L12: -1.4447 REMARK 3 L13: 0.2640 L23: 0.0416 REMARK 3 S TENSOR REMARK 3 S11: 0.0567 S12: 0.2305 S13: 0.8708 REMARK 3 S21: -0.0085 S22: 0.0547 S23: -0.2302 REMARK 3 S31: -0.3741 S32: 0.2052 S33: -0.0822 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.2850 16.9769 1.8522 REMARK 3 T TENSOR REMARK 3 T11: 0.1580 T22: 0.3119 REMARK 3 T33: 0.2642 T12: -0.0371 REMARK 3 T13: 0.0320 T23: -0.0120 REMARK 3 L TENSOR REMARK 3 L11: 2.3202 L22: 3.5817 REMARK 3 L33: 1.7838 L12: -0.2230 REMARK 3 L13: -0.6734 L23: -0.5413 REMARK 3 S TENSOR REMARK 3 S11: 0.1583 S12: -0.0788 S13: 0.0480 REMARK 3 S21: -0.0953 S22: 0.0501 S23: -0.0045 REMARK 3 S31: -0.0934 S32: 0.3255 S33: -0.2272 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0616 16.4512 6.5266 REMARK 3 T TENSOR REMARK 3 T11: 0.1608 T22: 0.1260 REMARK 3 T33: 0.1499 T12: 0.0043 REMARK 3 T13: -0.0136 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 1.0093 L22: 1.1598 REMARK 3 L33: 1.3185 L12: 0.3972 REMARK 3 L13: 0.0976 L23: 0.4668 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: 0.0269 S13: 0.0561 REMARK 3 S21: -0.0224 S22: 0.0204 S23: 0.0271 REMARK 3 S31: -0.1517 S32: -0.0153 S33: -0.0145 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.8378 9.7219 -5.1674 REMARK 3 T TENSOR REMARK 3 T11: 0.2712 T22: 0.3450 REMARK 3 T33: 0.2953 T12: -0.0558 REMARK 3 T13: -0.0448 T23: 0.0059 REMARK 3 L TENSOR REMARK 3 L11: 2.3236 L22: 6.6805 REMARK 3 L33: 5.4087 L12: -3.1432 REMARK 3 L13: -2.0499 L23: 1.0068 REMARK 3 S TENSOR REMARK 3 S11: 0.1793 S12: 0.7084 S13: -0.4627 REMARK 3 S21: -0.6366 S22: -0.0958 S23: 0.7008 REMARK 3 S31: 0.1866 S32: -0.8777 S33: -0.0373 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 536 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.8311 23.1529 -4.2508 REMARK 3 T TENSOR REMARK 3 T11: 0.3626 T22: 0.2813 REMARK 3 T33: 0.3177 T12: 0.0241 REMARK 3 T13: 0.0464 T23: -0.0586 REMARK 3 L TENSOR REMARK 3 L11: 3.5793 L22: 4.5238 REMARK 3 L33: 6.2160 L12: -0.8555 REMARK 3 L13: -0.6738 L23: 0.3278 REMARK 3 S TENSOR REMARK 3 S11: -0.3360 S12: 0.4380 S13: -0.5347 REMARK 3 S21: 0.2686 S22: -0.1525 S23: 0.1631 REMARK 3 S31: 0.8923 S32: 0.0386 S33: 0.3989 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 537 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.4597 11.6960 5.7968 REMARK 3 T TENSOR REMARK 3 T11: 0.1601 T22: 0.1433 REMARK 3 T33: 0.1570 T12: 0.0074 REMARK 3 T13: -0.0033 T23: 0.0096 REMARK 3 L TENSOR REMARK 3 L11: 1.2332 L22: 1.8923 REMARK 3 L33: 2.3227 L12: 0.2966 REMARK 3 L13: 0.2901 L23: 0.2637 REMARK 3 S TENSOR REMARK 3 S11: -0.0175 S12: 0.0047 S13: -0.0184 REMARK 3 S21: -0.0000 S22: 0.0336 S23: 0.0720 REMARK 3 S31: 0.0854 S32: -0.0796 S33: -0.0170 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 6DQ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234871. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-FEB-16 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-BM 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 MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28578 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 33.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.59300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 5IVB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 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 58.75300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.15450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.75300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.15450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 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 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 GLY A 353 REMARK 465 PHE A 354 REMARK 465 GLU A 355 REMARK 465 GLN A 356 REMARK 465 ALA A 357 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 27 CG CD OE1 OE2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 VAL A 65 CG1 CG2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 ARG A 69 CG CD NE CZ NH1 NH2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 ARG A 359 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 368 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 SER A 454 OG REMARK 470 VAL A 455 CG1 CG2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 ARG A 519 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 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 GLU A 23 79.82 -118.33 REMARK 500 PHE A 477 -8.22 81.30 REMARK 500 THR A 538 57.71 -99.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 902 DISTANCE = 6.11 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 UNEXPECTEDLY, WE DID NOT OBSERVE THE TERMINAL CYANO-3-METHYLBUT REMARK 600 MOIETY OF COMPOUND N45 (PDB CHEMICAL COMPONENT H6M) IN THE COMPLEX REMARK 600 STRUCTURE WITH KDM5A. IT IS UNCLEAR WHETHER EXPOSURE TO X-RAY REMARK 600 RADIATION INFLUENCES THE REACTIVITY OF THE CYANOACRYLATE GROUP OR REMARK 600 IF OTHER UNKNOWN CHEMICAL REACTIONS COULD OCCUR UNDER THE REMARK 600 CRYSTALLIZATION CONDITIONS. THE INHIBITOR IS MODELED AS IF SOME REMARK 600 HYDROLYSIS HAS OCCURRED. 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 89.0 REMARK 620 3 H6M A 601 N28 96.9 97.5 REMARK 620 4 H6M A 601 N29 88.9 174.9 78.2 REMARK 620 5 HOH A 714 O 91.5 78.5 170.7 106.1 REMARK 620 6 HOH A 726 O 170.5 86.7 92.1 96.1 79.4 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 H6M 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 EDO 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 DBREF 6DQ7 A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6DQ7 A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6DQ7 HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6DQ7 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 H6M A 601 29 HET MN A 602 1 HET EDO A 603 4 HET GOL A 604 6 HETNAM H6M N-{6-[4-(HYDROXYACETYL)-1,4-DIAZEPAN-1-YL]-2-(PYRIDIN- HETNAM 2 H6M 2-YL)PYRIMIDIN-4-YL}-BETA-ALANINE HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN H6M HYDROLYSIS PRODUCT OF 3-((6-(4-(2-CYANO-3-METHYLBUT-2- HETSYN 2 H6M ENOYL)-1,4-DIAZEPAN-1-YL)-2-(PYRIDIN-2-YL)PYRIMIDIN-4- HETSYN 3 H6M YL)AMINO)PROPANOIC ACID HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 H6M C19 H24 N6 O4 FORMUL 3 MN MN 2+ FORMUL 4 EDO C2 H6 O2 FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *202(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 LEU A 432 GLU A 434 5 3 HELIX 7 AA7 GLU A 435 LEU A 440 1 6 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 GLU A 527 5 5 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 SER A 491 GLY A 498 -1 N SER A 491 O THR A 565 SHEET 5 AA1 8 ASN A 579 VAL A 584 -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 TYR A 504 O SER A 572 SHEET 4 AA3 4 TYR A 553 GLN A 557 -1 O GLN A 557 N LYS A 501 LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.31 LINK OE2 GLU A 485 MN MN A 602 1555 1555 2.23 LINK N28 H6M A 601 MN MN A 602 1555 1555 2.41 LINK N29 H6M A 601 MN MN A 602 1555 1555 2.21 LINK MN MN A 602 O HOH A 714 1555 1555 2.17 LINK MN MN A 602 O HOH A 726 1555 1555 2.14 SITE 1 AC1 16 ARG A 73 TYR A 409 ALA A 411 ASP A 412 SITE 2 AC1 16 TYR A 472 SER A 479 PHE A 480 CYS A 481 SITE 3 AC1 16 HIS A 483 GLU A 485 ASP A 486 ASN A 493 SITE 4 AC1 16 LYS A 501 GLN A 535 MN A 602 HOH A 714 SITE 1 AC2 5 HIS A 483 GLU A 485 H6M A 601 HOH A 714 SITE 2 AC2 5 HOH A 726 SITE 1 AC3 5 LYS A 50 ARG A 52 ASN A 556 HOH A 763 SITE 2 AC3 5 HOH A 771 SITE 1 AC4 8 MET A 380 PRO A 381 GLU A 485 ASP A 486 SITE 2 AC4 8 HIS A 487 HOH A 712 HOH A 722 HOH A 809 CRYST1 117.506 62.309 46.695 90.00 92.39 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 0.008510 0.000000 0.000355 0.00000 SCALE2 0.000000 0.016049 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021434 0.00000