HEADER TRANSCRIPTION 14-MAR-07 2P54 TITLE A CRYSTAL STRUCTURE OF PPAR ALPHA BOUND WITH SRC1 PEPTIDE AND GW735 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PPAR ALPHA; COMPND 5 SYNONYM: PPAR-ALPHA; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NUCLEAR RECEPTOR COACTIVATOR 1; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: SRC1 PEPTIDE; COMPND 11 SYNONYM: NCOA-1, STEROID RECEPTOR COACTIVATOR 1, SRC-1, RIP160, COMPND 12 PROTEIN HIN-2, RENAL CARCINOMA ANTIGEN NY-REN-52; COMPND 13 EC: 2.3.1.48; COMPND 14 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: PPARA, NR1C1, PPAR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS PPAR ALPHA GW735 SRC1 AGONIST HDLC, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR R.X.XU,H.E.XU,M.L.SIERRA,V.G.MONTANA,M.H.LAMBERT,P.M.PIANETTI REVDAT 3 21-FEB-24 2P54 1 REMARK SEQADV REVDAT 2 24-FEB-09 2P54 1 VERSN REVDAT 1 24-APR-07 2P54 0 JRNL AUTH M.L.SIERRA,V.BENETON,A.B.BOULLAY,T.BOYER,A.BREWSTER, JRNL AUTH 2 F.DONCHE,M.C.FOREST,M.H.FOUCHET,F.J.GELLIBERT,D.A.GRILLOT, JRNL AUTH 3 M.H.LAMBERT,A.LAROZE,C.L.GRUMELEC,J.M.LINGET,V.G.MONTANA, JRNL AUTH 4 V.L.NGUYEN,E.NICODEME,V.PATEL,A.PENFORNIS,O.PINEAU,D.POHIN, JRNL AUTH 5 F.POTVAIN,G.PAULAIN,C.B.RUAULT,M.SAUNDERS,J.TOUM,H.E.XU, JRNL AUTH 6 R.X.XU,P.M.PIANETTI JRNL TITL SUBSTITUTED 2-[(4-AMINOMETHYL)PHENOXY]-2-METHYLPROPIONIC JRNL TITL 2 ACID PPAR AGONISTS. 1.DISCOVERY OF A NOVEL SERIES OF POTENT JRNL TITL 3 HDLC RAISING AGENTS. JRNL REF J.MED.CHEM. V. 50 685 2007 JRNL REFN ISSN 0022-2623 JRNL PMID 17243659 JRNL DOI 10.1021/JM058056X REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 29552 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) : 0.204 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1761 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 : 2196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 3.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01500 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.00500 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) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.287 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC 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 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: ML REMARK 4 REMARK 4 2P54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30145 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.240 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 39.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : 0.35000 REMARK 200 FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: APO PPAR ALPHA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7% PEG 3350, 200 MM NAF, 12% 2,5 REMARK 280 -HEXANEDIOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 30.63150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.76750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.63150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.76750 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 ASP A 202 CG OD1 OD2 REMARK 470 ASN A 235 CG OD1 ND2 REMARK 470 ASN A 261 CG OD1 ND2 REMARK 470 ASN A 393 CG OD1 ND2 REMARK 470 TYR A 468 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 686 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 688 CG CD CE NZ 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 LEU A 392 -64.27 -91.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 735 A 469 DBREF 2P54 A 202 468 UNP Q07869 PPARA_HUMAN 202 468 DBREF 2P54 B 686 696 UNP Q15788 NCOA1_HUMAN 686 696 SEQADV 2P54 ALA B 685 UNP Q15788 CLONING ARTIFACT SEQRES 1 A 267 ASP LEU LYS SER LEU ALA LYS ARG ILE TYR GLU ALA TYR SEQRES 2 A 267 LEU LYS ASN PHE ASN MET ASN LYS VAL LYS ALA ARG VAL SEQRES 3 A 267 ILE LEU SER GLY LYS ALA SER ASN ASN PRO PRO PHE VAL SEQRES 4 A 267 ILE HIS ASP MET GLU THR LEU CYS MET ALA GLU LYS THR SEQRES 5 A 267 LEU VAL ALA LYS LEU VAL ALA ASN GLY ILE GLN ASN LYS SEQRES 6 A 267 GLU ALA GLU VAL ARG ILE PHE HIS CYS CYS GLN CYS THR SEQRES 7 A 267 SER VAL GLU THR VAL THR GLU LEU THR GLU PHE ALA LYS SEQRES 8 A 267 ALA ILE PRO GLY PHE ALA ASN LEU ASP LEU ASN ASP GLN SEQRES 9 A 267 VAL THR LEU LEU LYS TYR GLY VAL TYR GLU ALA ILE PHE SEQRES 10 A 267 ALA MET LEU SER SER VAL MET ASN LYS ASP GLY MET LEU SEQRES 11 A 267 VAL ALA TYR GLY ASN GLY PHE ILE THR ARG GLU PHE LEU SEQRES 12 A 267 LYS SER LEU ARG LYS PRO PHE CYS ASP ILE MET GLU PRO SEQRES 13 A 267 LYS PHE ASP PHE ALA MET LYS PHE ASN ALA LEU GLU LEU SEQRES 14 A 267 ASP ASP SER ASP ILE SER LEU PHE VAL ALA ALA ILE ILE SEQRES 15 A 267 CYS CYS GLY ASP ARG PRO GLY LEU LEU ASN VAL GLY HIS SEQRES 16 A 267 ILE GLU LYS MET GLN GLU GLY ILE VAL HIS VAL LEU ARG SEQRES 17 A 267 LEU HIS LEU GLN SER ASN HIS PRO ASP ASP ILE PHE LEU SEQRES 18 A 267 PHE PRO LYS LEU LEU GLN LYS MET ALA ASP LEU ARG GLN SEQRES 19 A 267 LEU VAL THR GLU HIS ALA GLN LEU VAL GLN ILE ILE LYS SEQRES 20 A 267 LYS THR GLU SER ASP ALA ALA LEU HIS PRO LEU LEU GLN SEQRES 21 A 267 GLU ILE TYR ARG ASP MET TYR SEQRES 1 B 12 ALA ARG HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU HET 735 A 469 53 HETNAM 735 2-METHYL-2-(4-{[({4-METHYL-2-[4-(TRIFLUOROMETHYL) HETNAM 2 735 PHENYL]-1,3-THIAZOL-5-YL}CARBONYL) HETNAM 3 735 AMINO]METHYL}PHENOXY)PROPANOIC ACID FORMUL 3 735 C23 H21 F3 N2 O4 S FORMUL 4 HOH *268(H2 O) HELIX 1 1 SER A 205 PHE A 218 1 14 HELIX 2 2 ASN A 221 SER A 230 1 10 HELIX 3 3 ASP A 243 VAL A 255 1 13 HELIX 4 4 ALA A 256 ALA A 260 5 5 HELIX 5 5 GLY A 262 LYS A 266 5 5 HELIX 6 6 GLU A 267 ALA A 293 1 27 HELIX 7 7 GLY A 296 LEU A 300 5 5 HELIX 8 8 ASP A 301 SER A 322 1 22 HELIX 9 9 ARG A 341 LEU A 347 1 7 HELIX 10 10 PRO A 350 ILE A 354 5 5 HELIX 11 11 MET A 355 ALA A 367 1 13 HELIX 12 12 ASP A 371 CYS A 384 1 14 HELIX 13 13 ASN A 393 HIS A 416 1 24 HELIX 14 14 PHE A 421 GLU A 451 1 31 HELIX 15 15 HIS A 457 ARG A 465 1 9 HELIX 16 16 HIS B 687 GLU B 696 1 10 SHEET 1 A 4 PHE A 239 ILE A 241 0 SHEET 2 A 4 GLY A 337 THR A 340 1 O PHE A 338 N ILE A 241 SHEET 3 A 4 GLY A 329 VAL A 332 -1 N VAL A 332 O GLY A 337 SHEET 4 A 4 MET A 325 ASN A 326 -1 N ASN A 326 O GLY A 329 CISPEP 1 LYS A 349 PRO A 350 0 -0.16 SITE 1 AC1 16 ILE A 241 GLU A 251 VAL A 255 PHE A 273 SITE 2 AC1 16 CYS A 276 GLN A 277 THR A 279 SER A 280 SITE 3 AC1 16 TYR A 314 VAL A 332 ILE A 354 MET A 355 SITE 4 AC1 16 HIS A 440 LEU A 460 TYR A 464 HOH A 476 CRYST1 61.263 103.535 49.850 90.00 90.00 90.00 P 21 21 2 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 0.016323 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009659 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020060 0.00000