HEADER TRANSCRIPTION 14-SEP-19 6KXY TITLE HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH A SYNTHETIC TITLE 2 AGONIST (COMPOUND B) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PPAR-ALPHA,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PGC1ALPHA; COMPND 8 CHAIN: B; 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: 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS AGONIST, COMPLEX, NUCLEAR RECEPTOR, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.YOSHIDA,K.TACHIBANA,H.OKI,M.DOI,S.FUKUDA,T.YUZURIHA,R.TABATA, AUTHOR 2 K.ISHIMOTO,K.KAWAHARA,T.OHKUBO,H.MIYACHI,T.DOI REVDAT 2 22-NOV-23 6KXY 1 REMARK REVDAT 1 20-MAY-20 6KXY 0 JRNL AUTH T.YOSHIDA,H.OKI,M.DOI,S.FUKUDA,T.YUZURIHA,R.TABATA, JRNL AUTH 2 K.ISHIMOTO,K.KAWAHARA,T.OHKUBO,H.MIYACHI,T.DOI,K.TACHIBANA JRNL TITL STRUCTURAL BASIS FOR PPAR ALPHA ACTIVATION BY JRNL TITL 2 1H-PYRAZOLO-[3,4-B]PYRIDINE DERIVATIVES. JRNL REF SCI REP V. 10 7623 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32376995 JRNL DOI 10.1038/S41598-020-64527-X REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 20160 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.214 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2024 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 41.6810 - 4.8180 0.99 1399 162 0.2026 0.2172 REMARK 3 2 4.8180 - 3.8250 1.00 1334 137 0.1776 0.2043 REMARK 3 3 3.8250 - 3.3418 1.00 1332 128 0.1956 0.2349 REMARK 3 4 3.3418 - 3.0363 1.00 1283 163 0.2156 0.3331 REMARK 3 5 3.0363 - 2.8187 1.00 1310 141 0.2289 0.2903 REMARK 3 6 2.8187 - 2.6526 1.00 1293 140 0.2389 0.2826 REMARK 3 7 2.6526 - 2.5198 1.00 1282 139 0.2262 0.3098 REMARK 3 8 2.5198 - 2.4101 1.00 1289 152 0.2141 0.2717 REMARK 3 9 2.4101 - 2.3173 1.00 1251 155 0.2213 0.2622 REMARK 3 10 2.3173 - 2.2374 1.00 1294 144 0.2296 0.2979 REMARK 3 11 2.2374 - 2.1674 1.00 1256 138 0.2317 0.2778 REMARK 3 12 2.1674 - 2.1054 1.00 1261 158 0.2496 0.3292 REMARK 3 13 2.1054 - 2.0500 1.00 1272 150 0.2529 0.2829 REMARK 3 14 2.0500 - 2.0000 1.00 1280 117 0.2542 0.3298 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.30 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6KXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013823. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-19 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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20224 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.550 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 1.23800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1I7G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES-NAOH, PH 7.4, 19-23% PEG REMARK 280 4000, 19-23% 1,2-PROPANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 22.77400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.68450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.60150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.68450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.77400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.60150 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 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 GLY A 197 REMARK 465 GLY A 198 REMARK 465 GLN A 199 REMARK 465 THR A 200 REMARK 465 ALA A 201 REMARK 465 ASP A 202 REMARK 465 LEU A 203 REMARK 465 LYS A 204 REMARK 465 ALA A 233 REMARK 465 SER A 234 REMARK 465 ASN A 235 REMARK 465 LYS A 257 REMARK 465 LEU A 258 REMARK 465 VAL A 259 REMARK 465 ALA A 260 REMARK 465 ASN A 261 REMARK 465 GLY A 262 REMARK 465 ILE A 263 REMARK 465 TYR A 468 REMARK 465 PRO B 135 REMARK 465 GLN B 136 REMARK 465 GLU B 137 REMARK 465 ALA B 138 REMARK 465 GLU B 139 REMARK 465 GLU B 140 REMARK 465 ALA B 152 REMARK 465 ASN B 153 REMARK 465 THR B 154 REMARK 465 GLN B 155 REMARK 465 LEU B 156 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 ASN A 326 -168.38 -126.32 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 T06 A 501 DBREF 6KXY A 200 468 UNP Q07869 PPARA_HUMAN 200 468 DBREF 6KXY B 135 156 PDB 6KXY 6KXY 135 156 SEQADV 6KXY GLY A 197 UNP Q07869 EXPRESSION TAG SEQADV 6KXY GLY A 198 UNP Q07869 EXPRESSION TAG SEQADV 6KXY GLN A 199 UNP Q07869 EXPRESSION TAG SEQRES 1 A 272 GLY GLY GLN THR ALA ASP LEU LYS SER LEU ALA LYS ARG SEQRES 2 A 272 ILE TYR GLU ALA TYR LEU LYS ASN PHE ASN MET ASN LYS SEQRES 3 A 272 VAL LYS ALA ARG VAL ILE LEU SER GLY LYS ALA SER ASN SEQRES 4 A 272 ASN PRO PRO PHE VAL ILE HIS ASP MET GLU THR LEU CYS SEQRES 5 A 272 MET ALA GLU LYS THR LEU VAL ALA LYS LEU VAL ALA ASN SEQRES 6 A 272 GLY ILE GLN ASN LYS GLU ALA GLU VAL ARG ILE PHE HIS SEQRES 7 A 272 CYS CYS GLN CYS THR SER VAL GLU THR VAL THR GLU LEU SEQRES 8 A 272 THR GLU PHE ALA LYS ALA ILE PRO GLY PHE ALA ASN LEU SEQRES 9 A 272 ASP LEU ASN ASP GLN VAL THR LEU LEU LYS TYR GLY VAL SEQRES 10 A 272 TYR GLU ALA ILE PHE ALA MET LEU SER SER VAL MET ASN SEQRES 11 A 272 LYS ASP GLY MET LEU VAL ALA TYR GLY ASN GLY PHE ILE SEQRES 12 A 272 THR ARG GLU PHE LEU LYS SER LEU ARG LYS PRO PHE CYS SEQRES 13 A 272 ASP ILE MET GLU PRO LYS PHE ASP PHE ALA MET LYS PHE SEQRES 14 A 272 ASN ALA LEU GLU LEU ASP ASP SER ASP ILE SER LEU PHE SEQRES 15 A 272 VAL ALA ALA ILE ILE CYS CYS GLY ASP ARG PRO GLY LEU SEQRES 16 A 272 LEU ASN VAL GLY HIS ILE GLU LYS MET GLN GLU GLY ILE SEQRES 17 A 272 VAL HIS VAL LEU ARG LEU HIS LEU GLN SER ASN HIS PRO SEQRES 18 A 272 ASP ASP ILE PHE LEU PHE PRO LYS LEU LEU GLN LYS MET SEQRES 19 A 272 ALA ASP LEU ARG GLN LEU VAL THR GLU HIS ALA GLN LEU SEQRES 20 A 272 VAL GLN ILE ILE LYS LYS THR GLU SER ASP ALA ALA LEU SEQRES 21 A 272 HIS PRO LEU LEU GLN GLU ILE TYR ARG ASP MET TYR SEQRES 1 B 22 PRO GLN GLU ALA GLU GLU PRO SER LEU LEU LYS LYS LEU SEQRES 2 B 22 LEU LEU ALA PRO ALA ASN THR GLN LEU HET T06 A 501 26 HETNAM T06 6-ETHYL-1-(4-FLUOROPHENYL)-3-PENTAN-3-YL-PYRAZOLO[3,4- HETNAM 2 T06 B]PYRIDINE-4-CARBOXYLIC ACID FORMUL 3 T06 C20 H22 F N3 O2 FORMUL 4 HOH *85(H2 O) HELIX 1 AA1 SER A 205 PHE A 218 1 14 HELIX 2 AA2 ASN A 221 SER A 230 1 10 HELIX 3 AA3 ASP A 243 VAL A 255 1 13 HELIX 4 AA4 GLU A 267 ALA A 293 1 27 HELIX 5 AA5 ASP A 301 SER A 322 1 22 HELIX 6 AA6 SER A 323 MET A 325 5 3 HELIX 7 AA7 ARG A 341 LEU A 347 1 7 HELIX 8 AA8 PRO A 350 ILE A 354 5 5 HELIX 9 AA9 MET A 355 ALA A 367 1 13 HELIX 10 AB1 ASP A 371 CYS A 384 1 14 HELIX 11 AB2 ASN A 393 HIS A 416 1 24 HELIX 12 AB3 PHE A 421 GLU A 451 1 31 HELIX 13 AB4 HIS A 457 ARG A 465 1 9 HELIX 14 AB5 SER B 142 LEU B 149 1 8 SHEET 1 AA1 3 PHE A 239 ILE A 241 0 SHEET 2 AA1 3 GLY A 337 THR A 340 1 O PHE A 338 N ILE A 241 SHEET 3 AA1 3 GLY A 329 VAL A 332 -1 N VAL A 332 O GLY A 337 CISPEP 1 LYS A 349 PRO A 350 0 1.20 SITE 1 AC1 14 ILE A 272 PHE A 273 CYS A 276 GLN A 277 SITE 2 AC1 14 SER A 280 TYR A 314 LEU A 344 LEU A 347 SITE 3 AC1 14 ILE A 354 MET A 355 HIS A 440 VAL A 444 SITE 4 AC1 14 LEU A 456 TYR A 464 CRYST1 45.548 61.203 103.369 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 0.021955 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016339 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009674 0.00000