HEADER SERINE/THREONINE-PROTEIN KINASE 07-MAR-97 1IAN TITLE HUMAN P38 MAP KINASE INHIBITOR COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: P38 MAP KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CSBP, RK, P38; COMPND 5 EC: 2.7.1.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 CELL_LINE: B834; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: B834 (DE3) PLYSS KEYWDS PROTEIN SER/THR-KINASE, SERINE/THREONINE-PROTEIN KINASE, SERINE- KEYWDS 2 THREONINE-PROTEIN KINASE COMPLEX EXPDTA X-RAY DIFFRACTION MDLTYP CA ATOMS ONLY, CHAIN A AUTHOR L.TONG REVDAT 4 03-APR-24 1IAN 1 REMARK REVDAT 3 07-FEB-24 1IAN 1 REMARK REVDAT 2 24-FEB-09 1IAN 1 VERSN REVDAT 1 06-MAY-98 1IAN 0 JRNL AUTH L.TONG,S.PAV,D.M.WHITE,S.ROGERS,K.M.CRANE,C.L.CYWIN, JRNL AUTH 2 M.L.BROWN,C.A.PARGELLIS JRNL TITL A HIGHLY SPECIFIC INHIBITOR OF HUMAN P38 MAP KINASE BINDS IN JRNL TITL 2 THE ATP POCKET. JRNL REF NAT.STRUCT.BIOL. V. 4 311 1997 JRNL REFN ISSN 1072-8368 JRNL PMID 9095200 JRNL DOI 10.1038/NSB0497-311 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.CUENDA,J.ROUSE,Y.N.DOZA,R.MEIER,P.COHEN,T.F.GALLAGHER, REMARK 1 AUTH 2 P.R.YOUNG,J.C.LEE REMARK 1 TITL SB 203580 IS A SPECIFIC INHIBITOR OF A MAP KINASE HOMOLOGUE REMARK 1 TITL 2 WHICH IS STIMULATED BY CELLULAR STRESSES AND INTERLEUKIN-1 REMARK 1 REF FEBS LETT. V. 364 229 1995 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 1.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 24416 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1835 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 328 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.18000 REMARK 3 B22 (A**2) : 3.74000 REMARK 3 B33 (A**2) : -3.92000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.370 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IAN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25453 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : 0.04600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.15700 REMARK 200 R SYM FOR SHELL (I) : 0.15700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SE-MET MAD AND MR REMARK 200 SOFTWARE USED: MADSYS, X-PLOR 3.1 REMARK 200 STARTING MODEL: ERK2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.4 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 32.55000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.95000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.95000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.55000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.15000 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 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 MET A -5 REMARK 465 ALA A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 SER A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 4 REMARK 465 LYS A 118 REMARK 465 CYS A 119 REMARK 465 GLN A 120 REMARK 465 LYS A 121 REMARK 465 LEU A 122 REMARK 465 GLY A 170 REMARK 465 LEU A 171 REMARK 465 ALA A 172 REMARK 465 ARG A 173 REMARK 465 HIS A 174 REMARK 465 THR A 175 REMARK 465 ASP A 176 REMARK 465 ASP A 177 REMARK 465 GLU A 178 REMARK 465 MET A 179 REMARK 465 THR A 180 REMARK 465 GLY A 181 REMARK 465 TYR A 182 REMARK 465 VAL A 183 REMARK 465 ALA A 184 REMARK 465 LEU A 353 REMARK 465 ASP A 354 REMARK 465 GLN A 355 REMARK 465 GLU A 356 REMARK 465 GLU A 357 REMARK 465 MET A 358 REMARK 465 GLU A 359 REMARK 465 SER A 360 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D13 A 391 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE D13 A 393 DBREF 1IAN A 2 360 UNP Q16539 MK14_HUMAN 2 360 SEQRES 1 A 366 MET ALA HIS HIS HIS HIS HIS SER GLN GLU ARG PRO THR SEQRES 2 A 366 PHE TYR ARG GLN GLU LEU ASN LYS THR ILE TRP GLU VAL SEQRES 3 A 366 PRO GLU ARG TYR GLN ASN LEU SER PRO VAL GLY SER GLY SEQRES 4 A 366 ALA TYR GLY SER VAL CYS ALA ALA PHE ASP THR LYS THR SEQRES 5 A 366 GLY LEU ARG VAL ALA VAL LYS LYS LEU SER ARG PRO PHE SEQRES 6 A 366 GLN SER ILE ILE HIS ALA LYS ARG THR TYR ARG GLU LEU SEQRES 7 A 366 ARG LEU LEU LYS HIS MET LYS HIS GLU ASN VAL ILE GLY SEQRES 8 A 366 LEU LEU ASP VAL PHE THR PRO ALA ARG SER LEU GLU GLU SEQRES 9 A 366 PHE ASN ASP VAL TYR LEU VAL THR HIS LEU MET GLY ALA SEQRES 10 A 366 ASP LEU ASN ASN ILE VAL LYS CYS GLN LYS LEU THR ASP SEQRES 11 A 366 ASP HIS VAL GLN PHE LEU ILE TYR GLN ILE LEU ARG GLY SEQRES 12 A 366 LEU LYS TYR ILE HIS SER ALA ASP ILE ILE HIS ARG ASP SEQRES 13 A 366 LEU LYS PRO SER ASN LEU ALA VAL ASN GLU ASP CYS GLU SEQRES 14 A 366 LEU LYS ILE LEU ASP PHE GLY LEU ALA ARG HIS THR ASP SEQRES 15 A 366 ASP GLU MET THR GLY TYR VAL ALA THR ARG TRP TYR ARG SEQRES 16 A 366 ALA PRO GLU ILE MET LEU ASN TRP MET HIS TYR ASN GLN SEQRES 17 A 366 THR VAL ASP ILE TRP SER VAL GLY CYS ILE MET ALA GLU SEQRES 18 A 366 LEU LEU THR GLY ARG THR LEU PHE PRO GLY THR ASP HIS SEQRES 19 A 366 ILE ASP GLN LEU LYS LEU ILE LEU ARG LEU VAL GLY THR SEQRES 20 A 366 PRO GLY ALA GLU LEU LEU LYS LYS ILE SER SER GLU SER SEQRES 21 A 366 ALA ARG ASN TYR ILE GLN SER LEU THR GLN MET PRO LYS SEQRES 22 A 366 MET ASN PHE ALA ASN VAL PHE ILE GLY ALA ASN PRO LEU SEQRES 23 A 366 ALA VAL ASP LEU LEU GLU LYS MET LEU VAL LEU ASP SER SEQRES 24 A 366 ASP LYS ARG ILE THR ALA ALA GLN ALA LEU ALA HIS ALA SEQRES 25 A 366 TYR PHE ALA GLN TYR HIS ASP PRO ASP ASP GLU PRO VAL SEQRES 26 A 366 ALA ASP PRO TYR ASP GLN SER PHE GLU SER ARG ASP LEU SEQRES 27 A 366 LEU ILE ASP GLU TRP LYS SER LEU THR TYR ASP GLU VAL SEQRES 28 A 366 ILE SER PHE VAL PRO PRO PRO LEU ASP GLN GLU GLU MET SEQRES 29 A 366 GLU SER HET D13 A 391 27 HET D13 A 392 27 HET D13 A 393 27 HETNAM D13 4-[5-(3-IODO-PHENYL)-2-(4-METHANESULFINYL-PHENYL)-1H- HETNAM 2 D13 IMIDAZOL-4-YL]-PYRIDINE FORMUL 2 D13 3(C21 H16 I N3 O S) SITE 1 AC1 1 LEU A 108 SITE 1 AC2 1 SER A 254 CRYST1 65.100 74.300 77.900 90.00 90.00 90.00 P 21 21 21 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 0.015361 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012837 0.00000