HEADER OXIDOREDUCTASE/INHIBITOR 10-JUN-18 6DQ5 TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N43 I.E. 3-((6-(4- TITLE 2 ACRYLOYL-1,4-DIAZEPAN-1-YL)-2-(PYRIDIN-2-YL)PYRIMIDIN-4-YL)AMINO) TITLE 3 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 4 11-OCT-23 6DQ5 1 REMARK REVDAT 3 01-JAN-20 6DQ5 1 REMARK REVDAT 2 01-MAY-19 6DQ5 1 JRNL REVDAT 1 21-NOV-18 6DQ5 0 JRNL AUTH J.R.HORTON,C.B.WOODCOCK,Q.CHEN,X.LIU,X.ZHANG,J.SHANKS,G.RAI, JRNL AUTH 2 B.T.MOTT,D.J.JANSEN,S.C.KALES,M.J.HENDERSON,M.CYR,K.POHIDA, JRNL AUTH 3 X.HU,P.SHAH,X.XU,A.JADHAV,D.J.MALONEY,M.D.HALL,A.SIMEONOV, JRNL AUTH 4 H.FU,P.M.VERTINO,X.CHENG JRNL TITL STRUCTURE-BASED ENGINEERING OF IRREVERSIBLE INHIBITORS JRNL TITL 2 AGAINST HISTONE LYSINE DEMETHYLASE KDM5A. JRNL REF J. MED. CHEM. V. 61 10588 2018 JRNL REFN ISSN 1520-4804 JRNL PMID 30392349 JRNL DOI 10.1021/ACS.JMEDCHEM.8B01219 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. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.13_2998: ???) 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) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 25667 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1268 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 32.9699 - 3.9285 1.00 2881 157 0.1983 0.2034 REMARK 3 2 3.9285 - 3.1190 1.00 2845 146 0.2095 0.2510 REMARK 3 3 3.1190 - 2.7249 1.00 2837 151 0.2258 0.2355 REMARK 3 4 2.7249 - 2.4759 1.00 2839 134 0.2417 0.2985 REMARK 3 5 2.4759 - 2.2985 1.00 2809 164 0.2448 0.2657 REMARK 3 6 2.2985 - 2.1630 1.00 2818 144 0.2480 0.2815 REMARK 3 7 2.1630 - 2.0547 0.96 2728 128 0.2612 0.3222 REMARK 3 8 2.0547 - 1.9652 0.88 2483 130 0.2647 0.3065 REMARK 3 9 1.9652 - 1.8896 0.77 2159 114 0.2966 0.3480 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.350 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 2425 REMARK 3 ANGLE : 0.494 3326 REMARK 3 CHIRALITY : 0.041 347 REMARK 3 PLANARITY : 0.004 436 REMARK 3 DIHEDRAL : 12.406 1396 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 12 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.7747 2.2688 8.5130 REMARK 3 T TENSOR REMARK 3 T11: 0.2302 T22: 0.1884 REMARK 3 T33: 0.2601 T12: 0.0203 REMARK 3 T13: 0.0211 T23: -0.0100 REMARK 3 L TENSOR REMARK 3 L11: 5.2814 L22: 2.2808 REMARK 3 L33: 1.6796 L12: -0.8192 REMARK 3 L13: 1.1062 L23: 0.8548 REMARK 3 S TENSOR REMARK 3 S11: -0.0184 S12: 0.2968 S13: -0.2533 REMARK 3 S21: 0.1356 S22: 0.1862 S23: -0.4343 REMARK 3 S31: 0.0831 S32: 0.3541 S33: -0.1867 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 64 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.9848 6.8164 5.3166 REMARK 3 T TENSOR REMARK 3 T11: 0.1229 T22: 0.1697 REMARK 3 T33: 0.1801 T12: -0.0180 REMARK 3 T13: -0.0102 T23: 0.0153 REMARK 3 L TENSOR REMARK 3 L11: 2.0375 L22: 2.9347 REMARK 3 L33: 1.8226 L12: 0.5991 REMARK 3 L13: -0.0553 L23: 0.3036 REMARK 3 S TENSOR REMARK 3 S11: -0.0364 S12: 0.0788 S13: -0.1283 REMARK 3 S21: -0.1064 S22: 0.0318 S23: -0.1064 REMARK 3 S31: 0.0737 S32: 0.2963 S33: 0.0147 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 65 THROUGH 378 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.6225 27.4045 18.1553 REMARK 3 T TENSOR REMARK 3 T11: 0.2949 T22: 0.1696 REMARK 3 T33: 0.1554 T12: 0.0297 REMARK 3 T13: 0.0164 T23: -0.0221 REMARK 3 L TENSOR REMARK 3 L11: 1.7631 L22: 3.4933 REMARK 3 L33: 3.0255 L12: 0.5262 REMARK 3 L13: 0.1774 L23: -1.1617 REMARK 3 S TENSOR REMARK 3 S11: -0.0576 S12: -0.0332 S13: 0.1467 REMARK 3 S21: 0.2789 S22: 0.1028 S23: 0.0489 REMARK 3 S31: -0.5191 S32: -0.0661 S33: 0.0188 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 379 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.0370 15.0930 20.9202 REMARK 3 T TENSOR REMARK 3 T11: 0.2004 T22: 0.2606 REMARK 3 T33: 0.1544 T12: 0.0117 REMARK 3 T13: 0.0670 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: 0.4694 L22: 2.6676 REMARK 3 L33: 3.6673 L12: 0.8257 REMARK 3 L13: -0.0822 L23: 1.0698 REMARK 3 S TENSOR REMARK 3 S11: -0.1421 S12: 0.0173 S13: 0.0481 REMARK 3 S21: 0.2685 S22: 0.1252 S23: 0.2730 REMARK 3 S31: 0.1400 S32: -0.4853 S33: 0.0148 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 432 ) REMARK 3 ORIGIN FOR THE GROUP (A): -12.1708 26.3727 9.8640 REMARK 3 T TENSOR REMARK 3 T11: 0.2533 T22: 0.2381 REMARK 3 T33: 0.3880 T12: -0.0977 REMARK 3 T13: 0.0159 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 2.4873 L22: 0.4429 REMARK 3 L33: 1.4024 L12: -1.0736 REMARK 3 L13: -0.5623 L23: 0.3231 REMARK 3 S TENSOR REMARK 3 S11: -0.1360 S12: 0.3862 S13: 1.1040 REMARK 3 S21: 0.1028 S22: 0.1690 S23: -0.2201 REMARK 3 S31: -0.1664 S32: 0.2392 S33: -0.0231 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 447 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.8549 15.6321 7.2574 REMARK 3 T TENSOR REMARK 3 T11: 0.1844 T22: 0.3223 REMARK 3 T33: 0.2557 T12: -0.0637 REMARK 3 T13: 0.0219 T23: -0.0114 REMARK 3 L TENSOR REMARK 3 L11: 5.5096 L22: 3.3949 REMARK 3 L33: 2.4525 L12: 0.5931 REMARK 3 L13: 0.0707 L23: -0.3350 REMARK 3 S TENSOR REMARK 3 S11: 0.0966 S12: -0.8134 S13: -0.3657 REMARK 3 S21: 0.4098 S22: 0.0577 S23: -0.3090 REMARK 3 S31: -0.2176 S32: 0.4205 S33: -0.0642 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 448 THROUGH 474 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.1488 22.3738 -5.9918 REMARK 3 T TENSOR REMARK 3 T11: 0.6827 T22: 0.3439 REMARK 3 T33: 0.2468 T12: 0.0165 REMARK 3 T13: 0.0926 T23: 0.0888 REMARK 3 L TENSOR REMARK 3 L11: 0.7197 L22: 0.0801 REMARK 3 L33: 0.4658 L12: -0.1463 REMARK 3 L13: 0.5391 L23: -0.1511 REMARK 3 S TENSOR REMARK 3 S11: 0.5027 S12: 0.3215 S13: 0.3074 REMARK 3 S21: -0.7274 S22: 0.0196 S23: -0.0541 REMARK 3 S31: -0.8710 S32: 0.4102 S33: -0.4603 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 475 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.5731 15.2364 6.2850 REMARK 3 T TENSOR REMARK 3 T11: 0.1345 T22: 0.1424 REMARK 3 T33: 0.1407 T12: -0.0185 REMARK 3 T13: -0.0003 T23: 0.0123 REMARK 3 L TENSOR REMARK 3 L11: 0.8174 L22: 1.2403 REMARK 3 L33: 1.4765 L12: 0.0453 REMARK 3 L13: 0.7930 L23: 0.1785 REMARK 3 S TENSOR REMARK 3 S11: -0.0280 S12: 0.0296 S13: -0.0499 REMARK 3 S21: -0.0137 S22: 0.0435 S23: -0.0169 REMARK 3 S31: -0.0845 S32: 0.0691 S33: -0.0213 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 521 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.2169 9.5375 -5.2136 REMARK 3 T TENSOR REMARK 3 T11: 0.2722 T22: 0.3085 REMARK 3 T33: 0.2085 T12: -0.0532 REMARK 3 T13: -0.0685 T23: -0.0309 REMARK 3 L TENSOR REMARK 3 L11: 6.0684 L22: 6.3368 REMARK 3 L33: 3.7623 L12: -3.6353 REMARK 3 L13: -1.4043 L23: -0.7264 REMARK 3 S TENSOR REMARK 3 S11: 0.0200 S12: 0.5615 S13: -0.5083 REMARK 3 S21: -0.7091 S22: 0.1827 S23: 0.8479 REMARK 3 S31: 0.0864 S32: -0.6999 S33: -0.1177 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 522 THROUGH 537 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.6081 22.9992 -3.8895 REMARK 3 T TENSOR REMARK 3 T11: 0.2988 T22: 0.2713 REMARK 3 T33: 0.2892 T12: 0.0361 REMARK 3 T13: -0.0086 T23: -0.0718 REMARK 3 L TENSOR REMARK 3 L11: 5.2768 L22: 3.5828 REMARK 3 L33: 6.0630 L12: -0.3492 REMARK 3 L13: -2.5064 L23: -0.7555 REMARK 3 S TENSOR REMARK 3 S11: -0.4278 S12: 0.3738 S13: -0.5634 REMARK 3 S21: -0.2027 S22: -0.0029 S23: 0.0807 REMARK 3 S31: 0.5907 S32: 0.0297 S33: 0.5702 REMARK 3 TLS GROUP : 11 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 538 THROUGH 587 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.2430 11.5004 6.1298 REMARK 3 T TENSOR REMARK 3 T11: 0.1692 T22: 0.1087 REMARK 3 T33: 0.1270 T12: -0.0085 REMARK 3 T13: -0.0036 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.5857 L22: 1.4636 REMARK 3 L33: 1.5325 L12: 0.1629 REMARK 3 L13: 0.3749 L23: 0.2770 REMARK 3 S TENSOR REMARK 3 S11: 0.0115 S12: 0.0225 S13: -0.0326 REMARK 3 S21: -0.0441 S22: -0.0036 S23: 0.0630 REMARK 3 S31: 0.1480 S32: -0.0255 S33: -0.0064 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 6DQ5 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_1000234861. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-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 : 26638 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 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 (%) : 98.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.16300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.88500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 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 (%): 44.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 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 58.37450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.06700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.37450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.06700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 790 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 794 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 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 ASP A 462 REMARK 465 ILE A 463 REMARK 465 SER A 464 REMARK 465 GLY A 465 REMARK 465 MET A 466 REMARK 465 THR A 588 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 THR A 30 OG1 CG2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 ASP A 56 CG OD1 OD2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 ARG A 69 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 THR A 84 OG1 CG2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 GLU A 388 CG CD OE1 OE2 REMARK 470 LYS A 392 CG CD CE NZ REMARK 470 GLU A 402 CG CD OE1 OE2 REMARK 470 GLU A 403 CG CD OE1 OE2 REMARK 470 ASP A 404 CG OD1 OD2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 LYS A 425 CG CD CE NZ REMARK 470 ASP A 426 CG OD1 OD2 REMARK 470 ARG A 428 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 429 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 ILE A 431 CG1 CG2 CD1 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 HIS A 458 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 459 CG1 CG2 CD1 REMARK 470 VAL A 461 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 520 CG CD OE1 OE2 REMARK 470 LEU A 521 CG CD1 CD2 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 470 GLU A 547 CG CD OE1 OE2 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 64 84.40 -68.22 REMARK 500 PHE A 477 -8.96 80.32 REMARK 500 THR A 538 59.54 -113.23 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 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 483 NE2 REMARK 620 2 GLU A 485 OE2 89.9 REMARK 620 3 H6G A 601 N28 96.5 101.0 REMARK 620 4 H6G A 601 N29 91.4 175.7 74.8 REMARK 620 5 HOH A 725 O 93.3 80.9 170.0 103.2 REMARK 620 6 HOH A 734 O 171.5 87.2 91.8 92.1 78.4 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 H6G 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 DBREF 6DQ5 A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6DQ5 A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6DQ5 HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6DQ5 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 H6G A 601 29 HET MN A 602 1 HETNAM H6G N-[6-(4-ACRYLOYL-1,4-DIAZEPAN-1-YL)-2-(PYRIDIN-2-YL) HETNAM 2 H6G PYRIMIDIN-4-YL]-BETA-ALANINE HETNAM MN MANGANESE (II) ION FORMUL 2 H6G C20 H24 N6 O3 FORMUL 3 MN MN 2+ FORMUL 4 HOH *102(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 80 THR A 84 5 5 HELIX 4 AA4 LEU A 363 ASN A 379 1 17 HELIX 5 AA5 PRO A 381 VAL A 385 5 5 HELIX 6 AA6 PRO A 386 SER A 399 1 14 HELIX 7 AA7 SER A 415 GLY A 419 1 5 HELIX 8 AA8 LEU A 432 GLU A 434 5 3 HELIX 9 AA9 GLU A 435 LEU A 440 1 6 HELIX 10 AB1 ASN A 444 MET A 448 5 5 HELIX 11 AB2 SER A 454 ASN A 460 1 7 HELIX 12 AB3 GLU A 485 SER A 489 5 5 HELIX 13 AB4 PRO A 507 HIS A 509 5 3 HELIX 14 AB5 ALA A 510 ALA A 522 1 13 HELIX 15 AB6 PRO A 523 GLU A 527 5 5 HELIX 16 AB7 PRO A 530 GLN A 535 1 6 HELIX 17 AB8 LEU A 536 THR A 538 5 3 HELIX 18 AB9 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 TYR A 553 N GLY A 505 LINK NE2 HIS A 483 MN MN A 602 1555 1555 2.17 LINK OE2 GLU A 485 MN MN A 602 1555 1555 2.12 LINK N28 H6G A 601 MN MN A 602 1555 1555 2.37 LINK N29 H6G A 601 MN MN A 602 1555 1555 2.29 LINK MN MN A 602 O HOH A 725 1555 1555 2.13 LINK MN MN A 602 O HOH A 734 1555 1555 1.94 SITE 1 AC1 15 ARG A 73 TYR A 409 ALA A 411 ASP A 412 SITE 2 AC1 15 TYR A 472 SER A 479 PHE A 480 CYS A 481 SITE 3 AC1 15 HIS A 483 GLU A 485 ASN A 493 LYS A 501 SITE 4 AC1 15 MN A 602 HOH A 725 HOH A 734 SITE 1 AC2 5 HIS A 483 GLU A 485 H6G A 601 HOH A 725 SITE 2 AC2 5 HOH A 734 CRYST1 116.749 62.134 46.601 90.00 92.13 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 0.008565 0.000000 0.000319 0.00000 SCALE2 0.000000 0.016094 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021474 0.00000