HEADER OXIDOREDUCTASE/INHIBITOR 29-OCT-17 6BH5 TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-((2-CHLOROPHENYL)(3- TITLE 2 (PIPERIDIN-1-YL)PROPOXY)METHYL)-1H-PYRROLO[3,2-B]PYRIDINE-7- TITLE 3 CARBOXYLIC ACID (COMPOUND N48) 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 6BH5 1 LINK REVDAT 3 01-JAN-20 6BH5 1 REMARK REVDAT 2 25-APR-18 6BH5 1 JRNL REVDAT 1 28-MAR-18 6BH5 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. 1.65 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 39287 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1990 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 32.8475 - 3.9774 1.00 2785 147 0.1686 0.1799 REMARK 3 2 3.9774 - 3.1578 1.00 2714 146 0.1675 0.1843 REMARK 3 3 3.1578 - 2.7588 1.00 2706 142 0.1888 0.2216 REMARK 3 4 2.7588 - 2.5067 1.00 2729 139 0.2040 0.2393 REMARK 3 5 2.5067 - 2.3271 1.00 2694 141 0.2011 0.2193 REMARK 3 6 2.3271 - 2.1899 1.00 2714 132 0.1973 0.2301 REMARK 3 7 2.1899 - 2.0803 1.00 2677 162 0.1989 0.2298 REMARK 3 8 2.0803 - 1.9897 1.00 2689 132 0.2012 0.2159 REMARK 3 9 1.9897 - 1.9131 1.00 2700 164 0.2132 0.2158 REMARK 3 10 1.9131 - 1.8471 1.00 2670 128 0.2374 0.2624 REMARK 3 11 1.8471 - 1.7894 1.00 2695 137 0.2403 0.2693 REMARK 3 12 1.7894 - 1.7382 0.99 2641 150 0.2566 0.2560 REMARK 3 13 1.7382 - 1.6925 0.95 2564 146 0.2734 0.2704 REMARK 3 14 1.6925 - 1.6512 0.87 2319 124 0.3029 0.3691 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.720 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 2484 REMARK 3 ANGLE : 0.466 3392 REMARK 3 CHIRALITY : 0.042 347 REMARK 3 PLANARITY : 0.004 443 REMARK 3 DIHEDRAL : 13.333 1449 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.7300 4.6529 6.4361 REMARK 3 T TENSOR REMARK 3 T11: 0.1945 T22: 0.2144 REMARK 3 T33: 0.2244 T12: 0.0217 REMARK 3 T13: -0.0279 T23: 0.0112 REMARK 3 L TENSOR REMARK 3 L11: 0.8033 L22: 1.9401 REMARK 3 L33: 1.4268 L12: 0.5946 REMARK 3 L13: 0.2251 L23: 0.6736 REMARK 3 S TENSOR REMARK 3 S11: 0.0019 S12: 0.0417 S13: -0.1969 REMARK 3 S21: 0.0870 S22: 0.0997 S23: -0.2691 REMARK 3 S31: 0.1525 S32: 0.3305 S33: -0.1004 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5812 22.6248 19.1969 REMARK 3 T TENSOR REMARK 3 T11: 0.1934 T22: 0.1618 REMARK 3 T33: 0.1568 T12: 0.0194 REMARK 3 T13: 0.0200 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 1.2918 L22: 2.6864 REMARK 3 L33: 2.7612 L12: 0.4996 REMARK 3 L13: -0.0805 L23: 0.1706 REMARK 3 S TENSOR REMARK 3 S11: -0.0200 S12: -0.0922 S13: 0.0817 REMARK 3 S21: 0.2676 S22: -0.0192 S23: 0.1443 REMARK 3 S31: -0.1047 S32: -0.1850 S33: 0.0373 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 432 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.4995 26.7352 9.8792 REMARK 3 T TENSOR REMARK 3 T11: 0.2672 T22: 0.2979 REMARK 3 T33: 0.3608 T12: -0.0979 REMARK 3 T13: 0.0429 T23: -0.0554 REMARK 3 L TENSOR REMARK 3 L11: 1.8271 L22: 0.8408 REMARK 3 L33: 1.0414 L12: -0.1199 REMARK 3 L13: -0.5180 L23: -0.2722 REMARK 3 S TENSOR REMARK 3 S11: 0.0821 S12: 0.1635 S13: 0.6263 REMARK 3 S21: -0.0540 S22: 0.0726 S23: -0.3946 REMARK 3 S31: -0.2872 S32: 0.3274 S33: -0.1200 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 433 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): -5.1531 17.3621 2.3087 REMARK 3 T TENSOR REMARK 3 T11: 0.1590 T22: 0.3340 REMARK 3 T33: 0.2591 T12: -0.0460 REMARK 3 T13: 0.0544 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 1.8134 L22: 3.4815 REMARK 3 L33: 1.4138 L12: -0.3765 REMARK 3 L13: -0.4118 L23: 0.4702 REMARK 3 S TENSOR REMARK 3 S11: 0.1549 S12: 0.0625 S13: 0.1163 REMARK 3 S21: -0.1436 S22: 0.1264 S23: -0.0126 REMARK 3 S31: -0.2268 S32: 0.3991 S33: -0.2507 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 507 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.0132 16.6289 6.5710 REMARK 3 T TENSOR REMARK 3 T11: 0.1751 T22: 0.1443 REMARK 3 T33: 0.1379 T12: -0.0082 REMARK 3 T13: -0.0098 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.8357 L22: 0.7322 REMARK 3 L33: 0.7735 L12: 0.0888 REMARK 3 L13: 0.1456 L23: 0.5848 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: 0.0162 S13: 0.0493 REMARK 3 S21: 0.0048 S22: 0.0167 S23: 0.0112 REMARK 3 S31: -0.1484 S32: 0.0560 S33: 0.0124 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 508 THROUGH 547 ) REMARK 3 ORIGIN FOR THE GROUP (A): -38.3839 14.9854 -1.9472 REMARK 3 T TENSOR REMARK 3 T11: 0.2303 T22: 0.2559 REMARK 3 T33: 0.2685 T12: 0.0109 REMARK 3 T13: 0.0075 T23: -0.0273 REMARK 3 L TENSOR REMARK 3 L11: 0.5492 L22: 0.9078 REMARK 3 L33: 0.6990 L12: -0.0533 REMARK 3 L13: 0.1974 L23: -0.0797 REMARK 3 S TENSOR REMARK 3 S11: 0.0656 S12: 0.0689 S13: -0.0013 REMARK 3 S21: -0.1333 S22: -0.1046 S23: 0.2200 REMARK 3 S31: -0.0398 S32: -0.2343 S33: 0.0297 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 548 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.8899 12.0662 6.0545 REMARK 3 T TENSOR REMARK 3 T11: 0.1613 T22: 0.1372 REMARK 3 T33: 0.1407 T12: 0.0013 REMARK 3 T13: -0.0075 T23: 0.0131 REMARK 3 L TENSOR REMARK 3 L11: 0.9966 L22: 1.4337 REMARK 3 L33: 1.5260 L12: 0.1443 REMARK 3 L13: 0.0255 L23: 0.6367 REMARK 3 S TENSOR REMARK 3 S11: -0.0127 S12: 0.0231 S13: -0.0462 REMARK 3 S21: -0.0091 S22: 0.0075 S23: -0.0354 REMARK 3 S31: 0.0595 S32: 0.0354 S33: 0.0108 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 6BH5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230696. 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 : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39298 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 32.841 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 (%): 44.41 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 58.18500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.92150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.18500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.92150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 883 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 910 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 VAL A 358 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 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 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 ARG A 359 CG CD NE CZ NH1 NH2 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 LEU A 432 CG CD1 CD2 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 527 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 ASP A 412 66.09 -111.54 REMARK 500 PHE A 477 -8.29 80.61 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 97.7 REMARK 620 3 HIS A 571 NE2 86.0 88.3 REMARK 620 4 DNY A 601 N30 94.6 165.5 100.2 REMARK 620 5 HOH A 747 O 93.8 79.1 167.3 92.6 REMARK 620 6 HOH A 772 O 177.9 83.0 96.0 84.4 84.5 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 DNY 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 EDO A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 608 DBREF 6BH5 A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 6BH5 A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 6BH5 HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 6BH5 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 DNY A 601 30 HET MN A 602 1 HET EDO A 603 4 HET EDO A 604 4 HET EDO A 605 4 HET EDO A 606 4 HET EDO A 607 4 HET GOL A 608 6 HETNAM DNY 2-{(S)-(2-CHLOROPHENYL)[3-(PIPERIDIN-1-YL) HETNAM 2 DNY PROPOXY]METHYL}-1H-PYRROLO[3,2-B]PYRIDINE-7-CARBOXYLIC HETNAM 3 DNY ACID HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETNAM GOL GLYCEROL HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DNY C23 H26 CL N3 O3 FORMUL 3 MN MN 2+ FORMUL 4 EDO 5(C2 H6 O2) FORMUL 9 GOL C3 H8 O3 FORMUL 10 HOH *236(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 SER A 441 1 7 HELIX 10 AB1 ASN A 444 MET A 448 5 5 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 2.22 LINK OE2 GLU A 485 MN MN A 602 1555 1555 2.04 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.25 LINK N30 DNY A 601 MN MN A 602 1555 1555 2.25 LINK MN MN A 602 O HOH A 747 1555 1555 2.31 LINK MN MN A 602 O HOH A 772 1555 1555 2.10 SITE 1 AC1 15 TYR A 409 ALA A 411 TYR A 472 PHE A 480 SITE 2 AC1 15 CYS A 481 HIS A 483 ILE A 484 ASP A 486 SITE 3 AC1 15 ASN A 493 LYS A 501 TRP A 503 HIS A 571 SITE 4 AC1 15 MN A 602 HOH A 772 HOH A 807 SITE 1 AC2 6 HIS A 483 GLU A 485 HIS A 571 DNY A 601 SITE 2 AC2 6 HOH A 747 HOH A 772 SITE 1 AC3 6 MET A 380 PRO A 381 ASP A 486 HIS A 487 SITE 2 AC3 6 HOH A 742 HOH A 751 SITE 1 AC4 3 ARG A 52 ASN A 556 HOH A 744 SITE 1 AC5 2 GLU A 403 HOH A 815 SITE 1 AC6 3 MET A 384 HOH A 707 HOH A 755 SITE 1 AC7 2 TRP A 488 HOH A 801 SITE 1 AC8 10 LYS A 45 GLN A 75 ARG A 76 LEU A 77 SITE 2 AC8 10 GLU A 79 SER A 479 HOH A 701 HOH A 704 SITE 3 AC8 10 HOH A 719 HOH A 720 CRYST1 116.370 61.843 46.704 90.00 92.35 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 0.008593 0.000000 0.000352 0.00000 SCALE2 0.000000 0.016170 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021429 0.00000