HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 20-MAR-16 5IVC TITLE LINKED KDM5A JMJ DOMAIN BOUND TO THE INHIBITOR N3 (4'-[(2- TITLE 2 PHENYLETHYL)CARBAMOYL][2,2'-BIPYRIDINE]-4-CARBOXYLIC ACID) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 5A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LINKED KDM5A JMJ DOMAIN, UNP RESIDUES 1-87 AND 348-588; COMPND 5 SYNONYM: HISTONE DEMETHYLASE JARID1A,JUMONJI/ARID DOMAIN-CONTAINING COMPND 6 PROTEIN 1A,RETINOBLASTOMA-BINDING PROTEIN 2,RBBP-2; COMPND 7 EC: 1.14.11.-; COMPND 8 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 5IVC 1 REMARK REVDAT 2 03-AUG-16 5IVC 1 JRNL REVDAT 1 27-JUL-16 5IVC 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. 1.57 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 44784 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1992 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 36.9929 - 3.7891 0.99 3227 147 0.1499 0.1491 REMARK 3 2 3.7891 - 3.0079 0.99 3145 142 0.1425 0.1547 REMARK 3 3 3.0079 - 2.6278 0.99 3125 140 0.1522 0.1798 REMARK 3 4 2.6278 - 2.3876 0.98 3109 150 0.1662 0.1908 REMARK 3 5 2.3876 - 2.2165 0.98 3089 130 0.1599 0.1957 REMARK 3 6 2.2165 - 2.0858 0.97 3069 150 0.1552 0.1850 REMARK 3 7 2.0858 - 1.9814 0.98 3072 147 0.1532 0.1507 REMARK 3 8 1.9814 - 1.8951 0.97 3032 144 0.1623 0.1883 REMARK 3 9 1.8951 - 1.8222 0.97 3061 139 0.1879 0.2114 REMARK 3 10 1.8222 - 1.7593 0.97 3034 148 0.1942 0.2268 REMARK 3 11 1.7593 - 1.7043 0.97 3030 142 0.2114 0.2516 REMARK 3 12 1.7043 - 1.6556 0.97 3013 133 0.2356 0.2805 REMARK 3 13 1.6556 - 1.6120 0.96 3009 137 0.2846 0.3052 REMARK 3 14 1.6120 - 1.5727 0.89 2777 143 0.3468 0.3620 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) : 20.270 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 : 0.006 2597 REMARK 3 ANGLE : 0.781 3549 REMARK 3 CHIRALITY : 0.049 364 REMARK 3 PLANARITY : 0.005 469 REMARK 3 DIHEDRAL : 14.256 1506 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 12 THROUGH 355 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4703 14.0688 8.3767 REMARK 3 T TENSOR REMARK 3 T11: 0.1037 T22: 0.1102 REMARK 3 T33: 0.0685 T12: -0.0236 REMARK 3 T13: 0.0003 T23: 0.0368 REMARK 3 L TENSOR REMARK 3 L11: 1.4766 L22: 2.2184 REMARK 3 L33: 1.5275 L12: 0.0603 REMARK 3 L13: -0.0212 L23: 0.6290 REMARK 3 S TENSOR REMARK 3 S11: 0.0112 S12: -0.0043 S13: -0.0125 REMARK 3 S21: 0.0393 S22: 0.0447 S23: -0.1036 REMARK 3 S31: -0.0863 S32: 0.0879 S33: -0.0587 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 356 THROUGH 399 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.2161 20.8145 22.1781 REMARK 3 T TENSOR REMARK 3 T11: 0.1849 T22: 0.1116 REMARK 3 T33: 0.1076 T12: 0.0485 REMARK 3 T13: 0.0235 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 3.3832 L22: 2.3113 REMARK 3 L33: 3.0904 L12: 1.5561 REMARK 3 L13: 0.1567 L23: 0.6204 REMARK 3 S TENSOR REMARK 3 S11: -0.0129 S12: -0.1829 S13: 0.1851 REMARK 3 S21: 0.2957 S22: -0.0275 S23: 0.1276 REMARK 3 S31: -0.1248 S32: -0.0352 S33: -0.0056 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 400 THROUGH 459 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.8014 21.9412 5.3737 REMARK 3 T TENSOR REMARK 3 T11: 0.1609 T22: 0.1734 REMARK 3 T33: 0.1855 T12: -0.0548 REMARK 3 T13: 0.0154 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.5240 L22: 1.2155 REMARK 3 L33: 1.7548 L12: -1.0126 REMARK 3 L13: -0.4954 L23: 0.4574 REMARK 3 S TENSOR REMARK 3 S11: 0.0406 S12: 0.1200 S13: 0.1376 REMARK 3 S21: -0.0602 S22: -0.0053 S23: -0.1251 REMARK 3 S31: -0.2528 S32: 0.2340 S33: -0.0203 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 460 THROUGH 588 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.2598 14.8776 3.2486 REMARK 3 T TENSOR REMARK 3 T11: 0.1097 T22: 0.1034 REMARK 3 T33: 0.1177 T12: 0.0001 REMARK 3 T13: 0.0122 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 0.9455 L22: 1.1316 REMARK 3 L33: 1.7360 L12: -0.0668 REMARK 3 L13: 0.3506 L23: 0.3223 REMARK 3 S TENSOR REMARK 3 S11: 0.0169 S12: 0.0437 S13: -0.0348 REMARK 3 S21: -0.0240 S22: -0.0200 S23: 0.0810 REMARK 3 S31: -0.0607 S32: -0.0484 S33: 0.0012 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 5IVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6-9.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 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 : 44796 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 36.983 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.97100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 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 (%): 44.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 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 58.10800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.14750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.10800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 31.14750 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 931 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 THR A 344 REMARK 465 ARG A 345 REMARK 465 VAL A 346 REMARK 465 VAL A 461 REMARK 465 ASP A 462 REMARK 465 ILE A 463 REMARK 465 SER A 464 REMARK 465 GLY A 465 REMARK 465 MET A 466 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 12 CG CD OE1 OE2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 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 ARG A 347 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 349 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 350 CG CD OE1 OE2 REMARK 470 VAL A 358 CG1 CG2 REMARK 470 ARG A 359 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 392 CG CD CE NZ REMARK 470 LYS A 416 CG CD CE NZ REMARK 470 LYS A 430 CG CD CE NZ REMARK 470 GLU A 452 CG CD OE1 OE2 REMARK 470 ASN A 460 CG OD1 ND2 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: 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 854 O HOH A 914 1.91 REMARK 500 O HOH A 862 O HOH A 925 2.01 REMARK 500 O HOH A 950 O HOH A 966 2.10 REMARK 500 O HOH A 729 O HOH A 906 2.14 REMARK 500 O HOH A 766 O HOH A 934 2.16 REMARK 500 NH2 ARG A 76 O HOH A 701 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 975 O HOH A 977 4446 2.18 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 PHE A 477 -7.51 81.05 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 OE1 95.7 REMARK 620 3 HIS A 571 NE2 81.6 90.6 REMARK 620 4 6E7 A 601 N07 92.6 166.1 101.7 REMARK 620 5 6E7 A 601 N15 79.9 97.8 160.4 72.7 REMARK 620 6 HOH A 815 O 173.3 90.4 95.6 82.0 102.0 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 6E7 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 GOL A 606 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: 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 REMARK 900 RELATED ID: 5IWF RELATED DB: PDB DBREF 5IVC A 1 347 UNP P29375 KDM5A_HUMAN 1 87 DBREF 5IVC A 348 588 UNP P29375 KDM5A_HUMAN 348 588 SEQADV 5IVC HIS A -1 UNP P29375 EXPRESSION TAG SEQADV 5IVC 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 6E7 A 601 26 HET MN A 602 1 HET EDO A 603 5 HET EDO A 604 4 HET EDO A 605 4 HET GOL A 606 6 HETNAM 6E7 4'-[(2-PHENYLETHYL)CARBAMOYL][2,2'-BIPYRIDINE]-4- HETNAM 2 6E7 CARBOXYLIC 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 6E7 C20 H17 N3 O3 FORMUL 3 MN MN 2+ FORMUL 4 EDO 3(C2 H6 O2) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *278(H2 O) HELIX 1 AA1 ASP A 31 GLU A 44 1 14 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 SER A 441 1 7 HELIX 8 AA8 ASN A 444 MET A 448 5 5 HELIX 9 AA9 SER A 454 ASN A 460 1 7 HELIX 10 AB1 GLU A 485 SER A 489 5 5 HELIX 11 AB2 PRO A 507 HIS A 509 5 3 HELIX 12 AB3 ALA A 510 ALA A 522 1 13 HELIX 13 AB4 PRO A 523 GLU A 527 5 5 HELIX 14 AB5 PRO A 530 GLN A 535 1 6 HELIX 15 AB6 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 TYR A 472 O ALA A 581 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 TYR A 570 ASN A 575 -1 O GLY A 573 N PHE A 480 SHEET 3 AA3 4 LYS A 501 VAL A 506 -1 N THR A 502 O PHE A 574 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 2.26 LINK OE1 GLU A 485 MN MN A 602 1555 1555 2.06 LINK NE2 HIS A 571 MN MN A 602 1555 1555 2.29 LINK N07 6E7 A 601 MN MN A 602 1555 1555 2.25 LINK N15 6E7 A 601 MN MN A 602 1555 1555 2.24 LINK MN MN A 602 O HOH A 815 1555 1555 2.22 SITE 1 AC1 12 ARG A 73 TYR A 409 TYR A 472 SER A 479 SITE 2 AC1 12 PHE A 480 HIS A 483 GLU A 485 LYS A 501 SITE 3 AC1 12 TRP A 503 HIS A 571 MN A 602 HOH A 815 SITE 1 AC2 5 HIS A 483 GLU A 485 HIS A 571 6E7 A 601 SITE 2 AC2 5 HOH A 815 SITE 1 AC3 4 LYS A 45 ARG A 73 HIS A 509 HOH A 803 SITE 1 AC4 4 GLU A 64 VAL A 65 LYS A 66 ARG A 429 SITE 1 AC5 6 SER A 399 ILE A 539 MET A 540 ASN A 541 SITE 2 AC5 6 HOH A 778 HOH A 806 SITE 1 AC6 9 MET A 380 PRO A 381 GLU A 485 ASP A 486 SITE 2 AC6 9 HIS A 487 TRP A 488 HOH A 703 HOH A 718 SITE 3 AC6 9 HOH A 898 CRYST1 116.216 62.295 46.519 90.00 92.18 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 0.008605 0.000000 0.000328 0.00000 SCALE2 0.000000 0.016053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021512 0.00000