HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 22-MAR-16 5IWF TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR 2-(((2-((2- TITLE 2 (DIMETHYLAMINO)ETHYL)(ETHYL)AMINO)-2-OXOETHYL)AMINO)METHYL) TITLE 3 ISONICOTINAMID COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5A,LYSINE-SPECIFIC DEMETHYLASE COMPND 3 5A; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: LINKED KDM5A JMJ DOMAIN, UNP RESIDUES 1-87 AND 348-588; COMPND 6 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 7 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2,HISTONE COMPND 8 DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING PROTEIN 1A, COMPND 9 RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2; COMPND 10 EC: 1.14.11.-; COMPND 11 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 EXPDTA X-RAY DIFFRACTION AUTHOR J.R.HORTON,X.CHENG REVDAT 3 27-SEP-23 5IWF 1 REMARK REVDAT 2 03-AUG-16 5IWF 1 JRNL REVDAT 1 27-JUL-16 5IWF 0 JRNL AUTH J.R.HORTON,X.LIU,M.GALE,L.WU,J.R.SHANKS,X.ZHANG,P.J.WEBBER, JRNL AUTH 2 J.S.BELL,S.C.KALES,B.T.MOTT,G.RAI,D.J.JANSEN,M.J.HENDERSON, JRNL AUTH 3 D.J.URBAN,M.D.HALL,A.SIMEONOV,D.J.MALONEY,M.A.JOHNS,H.FU, JRNL AUTH 4 A.JADHAV,P.M.VERTINO,Q.YAN,X.CHENG JRNL TITL STRUCTURAL BASIS FOR KDM5A HISTONE LYSINE DEMETHYLASE JRNL TITL 2 INHIBITION BY DIVERSE COMPOUNDS. JRNL REF CELL CHEM BIOL V. 23 769 2016 JRNL REFN ESSN 2451-9456 JRNL PMID 27427228 JRNL DOI 10.1016/J.CHEMBIOL.2016.06.006 REMARK 1 REMARK 1 REFERENCE 1 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. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 14531 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 728 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 32.9979 - 3.9130 0.99 2770 147 0.1605 0.1952 REMARK 3 2 3.9130 - 3.1066 0.89 2530 137 0.2070 0.2785 REMARK 3 3 3.1066 - 2.7141 1.00 2895 146 0.2069 0.2759 REMARK 3 4 2.7141 - 2.4661 1.00 2843 151 0.2124 0.2432 REMARK 3 5 2.4661 - 2.2894 0.97 2765 147 0.2122 0.2717 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.170 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 : 0.003 2416 REMARK 3 ANGLE : 0.664 3310 REMARK 3 CHIRALITY : 0.046 345 REMARK 3 PLANARITY : 0.005 434 REMARK 3 DIHEDRAL : 12.726 1396 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 62 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.1862 4.6366 6.5735 REMARK 3 T TENSOR REMARK 3 T11: 0.2470 T22: 0.2006 REMARK 3 T33: 0.2396 T12: 0.0068 REMARK 3 T13: -0.0064 T23: 0.0088 REMARK 3 L TENSOR REMARK 3 L11: 1.9941 L22: 2.7520 REMARK 3 L33: 2.5542 L12: 0.5357 REMARK 3 L13: 0.8771 L23: 1.1040 REMARK 3 S TENSOR REMARK 3 S11: 0.0292 S12: 0.1543 S13: -0.3254 REMARK 3 S21: -0.1357 S22: 0.1917 S23: -0.3253 REMARK 3 S31: 0.0648 S32: 0.4421 S33: -0.2503 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 63 THROUGH 405 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.2082 23.5724 19.0324 REMARK 3 T TENSOR REMARK 3 T11: 0.2801 T22: 0.1618 REMARK 3 T33: 0.1754 T12: 0.0514 REMARK 3 T13: 0.0324 T23: -0.0001 REMARK 3 L TENSOR REMARK 3 L11: 3.4091 L22: 3.2633 REMARK 3 L33: 2.9736 L12: 0.4936 REMARK 3 L13: 0.3443 L23: 0.8679 REMARK 3 S TENSOR REMARK 3 S11: -0.1364 S12: 0.0482 S13: 0.4233 REMARK 3 S21: 0.1459 S22: 0.0867 S23: 0.2337 REMARK 3 S31: -0.3687 S32: -0.2780 S33: 0.0595 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 406 THROUGH 469 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.7184 21.8291 5.3624 REMARK 3 T TENSOR REMARK 3 T11: 0.2882 T22: 0.2987 REMARK 3 T33: 0.2824 T12: -0.0728 REMARK 3 T13: 0.0524 T23: 0.0170 REMARK 3 L TENSOR REMARK 3 L11: 2.3001 L22: 1.4280 REMARK 3 L33: 2.0691 L12: -1.2935 REMARK 3 L13: -2.0445 L23: 0.7299 REMARK 3 S TENSOR REMARK 3 S11: 0.2249 S12: 0.1965 S13: 0.2756 REMARK 3 S21: -0.1785 S22: -0.1314 S23: -0.1127 REMARK 3 S31: -0.2637 S32: 0.2022 S33: -0.0386 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 470 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.8250 14.6131 3.8036 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.0941 REMARK 3 T33: 0.1157 T12: -0.0080 REMARK 3 T13: 0.0226 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 1.8636 L22: 2.3474 REMARK 3 L33: 2.6936 L12: 0.3275 REMARK 3 L13: 0.4268 L23: 0.4135 REMARK 3 S TENSOR REMARK 3 S11: 0.0334 S12: 0.0741 S13: 0.0688 REMARK 3 S21: -0.1013 S22: 0.0035 S23: 0.1533 REMARK 3 S31: -0.0160 S32: -0.1241 S33: -0.0288 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 5IWF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-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) : 1.0000 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 : 14593 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.289 REMARK 200 RESOLUTION RANGE LOW (A) : 32.994 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.56900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.500 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 (%): 44.87 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 58.53350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.95900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.53350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.95900 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 791 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 THR A 344 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 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 GLU A 44 CG CD OE1 OE2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 GLN A 58 CG CD OE1 NE2 REMARK 470 GLU A 64 CG CD OE1 OE2 REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 SER A 67 OG REMARK 470 PHE A 354 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 355 CG CD OE1 OE2 REMARK 470 GLN A 356 CG CD OE1 NE2 REMARK 470 GLU A 368 CG CD OE1 OE2 REMARK 470 GLU A 388 CG CD OE1 OE2 REMARK 470 LYS A 392 CG CD CE NZ REMARK 470 ILE A 401 CG1 CG2 CD1 REMARK 470 GLU A 402 CG CD OE1 OE2 REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 ASP A 417 CG OD1 OD2 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 GLN A 453 CG CD OE1 NE2 REMARK 470 VAL A 455 CG1 CG2 REMARK 470 LYS A 467 CG CD CE NZ REMARK 470 GLU A 512 CG CD OE1 OE2 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 470 ILE A 539 CG1 CG2 CD1 REMARK 470 GLU A 547 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 704 O HOH A 714 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 430 -120.61 50.13 REMARK 500 ILE A 431 69.27 60.48 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 92.2 REMARK 620 3 HIS A 571 NE2 78.3 84.9 REMARK 620 4 LQT A 601 N06 94.4 167.0 107.3 REMARK 620 5 LQT A 601 N09 79.2 97.9 157.4 72.5 REMARK 620 6 HOH A 742 O 177.8 88.5 99.7 85.3 102.8 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 LQT 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ISL RELATED DB: PDB REMARK 900 RELATED ID: 5IVB RELATED DB: PDB REMARK 900 RELATED ID: 5IVC RELATED DB: PDB REMARK 900 RELATED ID: 5IVE RELATED DB: PDB REMARK 900 RELATED ID: 5IVF RELATED DB: PDB REMARK 900 RELATED ID: 5IVJ RELATED DB: PDB REMARK 900 RELATED ID: 5IVV RELATED DB: PDB REMARK 900 RELATED ID: 5IVY RELATED DB: PDB REMARK 900 RELATED ID: 5IW0 RELATED DB: PDB DBREF 5IWF A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 5IWF A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 5IWF HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 5IWF 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 LQT A 601 22 HET MN A 602 1 HETNAM LQT 2-[[[2-[2-(DIMETHYLAMINO)ETHYL-ETHYL-AMINO]-2- HETNAM 2 LQT OXIDANYLIDENE-ETHYL]AMINO]METHYL]PYRIDINE-4- HETNAM 3 LQT CARBOXAMIDE HETNAM MN MANGANESE (II) ION HETSYN LQT KDOAM25A FORMUL 2 LQT C15 H25 N5 O2 FORMUL 3 MN MN 2+ FORMUL 4 HOH *101(H2 O) HELIX 1 AA1 ASP A 31 GLY A 47 1 17 HELIX 2 AA2 LEU A 363 ASN A 379 1 17 HELIX 3 AA3 PRO A 381 VAL A 385 5 5 HELIX 4 AA4 PRO A 386 SER A 400 1 15 HELIX 5 AA5 SER A 415 GLY A 419 1 5 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 THR A 538 1 9 HELIX 14 AB5 ASN A 541 HIS A 548 1 8 SHEET 1 AA1 7 VAL A 21 PHE A 22 0 SHEET 2 AA1 7 ILE A 48 ILE A 51 1 O LYS A 50 N PHE A 22 SHEET 3 AA1 7 PHE A 562 THR A 565 -1 O PHE A 562 N ILE A 51 SHEET 4 AA1 7 TYR A 490 GLY A 498 -1 N SER A 491 O THR A 565 SHEET 5 AA1 7 ASN A 579 PHE A 586 -1 O GLU A 582 N TYR A 494 SHEET 6 AA1 7 TRP A 470 GLY A 474 -1 N TRP A 470 O ALA A 583 SHEET 7 AA1 7 ILE A 413 SER A 414 -1 N ILE A 413 O LEU A 471 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 2 ARG A 73 ARG A 76 0 SHEET 2 AA3 2 ILE A 406 TYR A 409 -1 O VAL A 407 N GLN A 75 SHEET 1 AA4 4 SER A 479 HIS A 483 0 SHEET 2 AA4 4 HIS A 571 ASN A 575 -1 O GLY A 573 N PHE A 480 SHEET 3 AA4 4 LYS A 501 GLY A 505 -1 N THR A 502 O PHE A 574 SHEET 4 AA4 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 2.30 LINK OE2 GLU A 485 MN MN A 602 1555 1555 1.98 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.39 LINK N06 LQT A 601 MN MN A 602 1555 1555 2.33 LINK N09 LQT A 601 MN MN A 602 1555 1555 2.41 LINK MN MN A 602 O HOH A 742 1555 1555 2.26 CISPEP 1 CYS A 476 PHE A 477 0 -4.99 SITE 1 AC1 13 TYR A 409 TRP A 470 TYR A 472 PHE A 480 SITE 2 AC1 13 HIS A 483 GLU A 485 ASP A 486 LYS A 501 SITE 3 AC1 13 TRP A 503 VAL A 584 ASN A 585 MN A 602 SITE 4 AC1 13 HOH A 724 SITE 1 AC2 5 HIS A 483 GLU A 485 HIS A 571 LQT A 601 SITE 2 AC2 5 HOH A 742 CRYST1 117.067 61.918 46.751 90.00 92.28 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 0.008542 0.000000 0.000340 0.00000 SCALE2 0.000000 0.016150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021407 0.00000