HEADER TRANSCRIPTION 18-FEB-21 7E5G TITLE HUMAN PPAR ALPHA LIGAND BINDING DOMAIN IN COMPLEX WITH YN4PAI OBTAINED TITLE 2 BY SOAKING COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR ALPHA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A KEYWDS NUCLEAR RECEPTOR, PPAR, PROTEIN-LIGAND COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR T.OYAMA,S.KAMATA,I.ISHII,H.MIYACHI REVDAT 2 29-NOV-23 7E5G 1 REMARK REVDAT 1 06-OCT-21 7E5G 0 JRNL AUTH T.OYAMA,S.KAMATA,I.ISHII,H.MIYACHI JRNL TITL CRYSTAL STRUCTURES OF THE HUMAN PEROXISOME JRNL TITL 2 PROLIFERATOR-ACTIVATED RECEPTOR (PPAR) ALPHA LIGAND-BINDING JRNL TITL 3 DOMAIN IN COMPLEXES WITH A SERIES OF PHENYLPROPANOIC ACID JRNL TITL 4 DERIVATIVES GENERATED BY A LIGAND-EXCHANGE SOAKING METHOD. JRNL REF BIOL.PHARM.BULL. V. 44 1202 2021 JRNL REFN ISSN 0918-6158 JRNL PMID 34471048 JRNL DOI 10.1248/BPB.B21-00220 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 63155 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 3080 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 43.0700 - 4.6500 0.98 2780 129 0.1648 0.1792 REMARK 3 2 4.6500 - 3.6900 0.99 2769 148 0.1606 0.1664 REMARK 3 3 3.6900 - 3.2300 0.99 2767 150 0.1954 0.1885 REMARK 3 4 3.2200 - 2.9300 0.99 2745 167 0.2203 0.2408 REMARK 3 5 2.9300 - 2.7200 0.99 2806 143 0.2087 0.2601 REMARK 3 6 2.7200 - 2.5600 0.99 2793 127 0.2135 0.2435 REMARK 3 7 2.5600 - 2.4300 0.99 2790 152 0.2044 0.2176 REMARK 3 8 2.4300 - 2.3300 0.99 2712 163 0.1929 0.2302 REMARK 3 9 2.3300 - 2.2400 0.96 2675 141 0.2014 0.2636 REMARK 3 10 2.2400 - 2.1600 0.96 2746 124 0.2024 0.2121 REMARK 3 11 2.1600 - 2.0900 0.98 2746 126 0.2062 0.2361 REMARK 3 12 2.0900 - 2.0300 0.99 2746 160 0.2363 0.2507 REMARK 3 13 2.0300 - 1.9800 0.96 2717 125 0.2301 0.2817 REMARK 3 14 1.9800 - 1.9300 0.94 2622 146 0.2302 0.2705 REMARK 3 15 1.9300 - 1.8900 0.95 2672 105 0.2306 0.2136 REMARK 3 16 1.8900 - 1.8500 0.96 2708 123 0.2260 0.2742 REMARK 3 17 1.8500 - 1.8100 0.97 2704 129 0.2300 0.3644 REMARK 3 18 1.8100 - 1.7700 0.97 2696 154 0.2421 0.3217 REMARK 3 19 1.7700 - 1.7400 0.97 2714 172 0.2472 0.3074 REMARK 3 20 1.7400 - 1.7100 0.98 2713 129 0.2606 0.2608 REMARK 3 21 1.7100 - 1.6900 0.97 2789 131 0.2753 0.3001 REMARK 3 22 1.6900 - 1.6600 0.98 2665 136 0.2793 0.3215 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) : 0.207 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.907 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.79 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 : 0.005 2201 REMARK 3 ANGLE : 0.758 2976 REMARK 3 CHIRALITY : 0.043 337 REMARK 3 PLANARITY : 0.005 380 REMARK 3 DIHEDRAL : 11.802 845 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 7E5G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1300020799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 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 : FIXED EXIT SI DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : TWO DIMENSIONAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63155 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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: 2ZNN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 25% (W/V) POLYETHYLENE REMARK 280 GLYCOL (PEG) 3350, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.90150 REMARK 290 SMTRY3 2 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 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -30.90150 REMARK 350 BIOMT3 2 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 196 REMARK 465 SER A 197 REMARK 465 HIS A 198 REMARK 465 MET A 199 REMARK 465 LYS A 232 REMARK 465 ALA A 233 REMARK 465 SER A 234 REMARK 465 ASN A 235 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 THR A 200 OG1 CG2 REMARK 470 ASN A 236 CG OD1 ND2 REMARK 470 ILE A 263 CG1 CG2 CD1 REMARK 470 GLN A 264 CD OE1 NE2 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 393 72.68 -105.78 REMARK 500 MET A 467 -73.34 -83.74 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 HVX A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VI8 RELATED DB: PDB DBREF 7E5G A 200 468 UNP Q07869 PPARA_HUMAN 200 468 SEQADV 7E5G GLY A 196 UNP Q07869 EXPRESSION TAG SEQADV 7E5G SER A 197 UNP Q07869 EXPRESSION TAG SEQADV 7E5G HIS A 198 UNP Q07869 EXPRESSION TAG SEQADV 7E5G MET A 199 UNP Q07869 EXPRESSION TAG SEQRES 1 A 273 GLY SER HIS MET THR ALA ASP LEU LYS SER LEU ALA LYS SEQRES 2 A 273 ARG ILE TYR GLU ALA TYR LEU LYS ASN PHE ASN MET ASN SEQRES 3 A 273 LYS VAL LYS ALA ARG VAL ILE LEU SER GLY LYS ALA SER SEQRES 4 A 273 ASN ASN PRO PRO PHE VAL ILE HIS ASP MET GLU THR LEU SEQRES 5 A 273 CYS MET ALA GLU LYS THR LEU VAL ALA LYS LEU VAL ALA SEQRES 6 A 273 ASN GLY ILE GLN ASN LYS GLU ALA GLU VAL ARG ILE PHE SEQRES 7 A 273 HIS CYS CYS GLN CYS THR SER VAL GLU THR VAL THR GLU SEQRES 8 A 273 LEU THR GLU PHE ALA LYS ALA ILE PRO GLY PHE ALA ASN SEQRES 9 A 273 LEU ASP LEU ASN ASP GLN VAL THR LEU LEU LYS TYR GLY SEQRES 10 A 273 VAL TYR GLU ALA ILE PHE ALA MET LEU SER SER VAL MET SEQRES 11 A 273 ASN LYS ASP GLY MET LEU VAL ALA TYR GLY ASN GLY PHE SEQRES 12 A 273 ILE THR ARG GLU PHE LEU LYS SER LEU ARG LYS PRO PHE SEQRES 13 A 273 CYS ASP ILE MET GLU PRO LYS PHE ASP PHE ALA MET LYS SEQRES 14 A 273 PHE ASN ALA LEU GLU LEU ASP ASP SER ASP ILE SER LEU SEQRES 15 A 273 PHE VAL ALA ALA ILE ILE CYS CYS GLY ASP ARG PRO GLY SEQRES 16 A 273 LEU LEU ASN VAL GLY HIS ILE GLU LYS MET GLN GLU GLY SEQRES 17 A 273 ILE VAL HIS VAL LEU ARG LEU HIS LEU GLN SER ASN HIS SEQRES 18 A 273 PRO ASP ASP ILE PHE LEU PHE PRO LYS LEU LEU GLN LYS SEQRES 19 A 273 MET ALA ASP LEU ARG GLN LEU VAL THR GLU HIS ALA GLN SEQRES 20 A 273 LEU VAL GLN ILE ILE LYS LYS THR GLU SER ASP ALA ALA SEQRES 21 A 273 LEU HIS PRO LEU LEU GLN GLU ILE TYR ARG ASP MET TYR HET HVX A 501 38 HETNAM HVX (2S)-2-[[4-BUTOXY-3-[(PYREN-1-YLCARBONYLAMINO) HETNAM 2 HVX METHYL]PHENYL]METHYL]BUTANOIC ACID FORMUL 2 HVX C33 H33 N O4 FORMUL 3 HOH *113(H2 O) HELIX 1 AA1 THR A 200 PHE A 218 1 19 HELIX 2 AA2 ASN A 221 GLY A 231 1 11 HELIX 3 AA3 ASP A 243 VAL A 255 1 13 HELIX 4 AA4 ALA A 256 ALA A 260 5 5 HELIX 5 AA5 ASN A 261 ASN A 265 5 5 HELIX 6 AA6 GLU A 267 ALA A 291 1 25 HELIX 7 AA7 LYS A 292 ILE A 294 5 3 HELIX 8 AA8 ASP A 301 SER A 322 1 22 HELIX 9 AA9 ARG A 341 SER A 346 1 6 HELIX 10 AB1 PRO A 350 ILE A 354 5 5 HELIX 11 AB2 MET A 355 ALA A 367 1 13 HELIX 12 AB3 ASP A 371 CYS A 384 1 14 HELIX 13 AB4 ASN A 393 HIS A 416 1 24 HELIX 14 AB5 PHE A 421 GLU A 451 1 31 HELIX 15 AB6 HIS A 457 ARG A 465 1 9 SHEET 1 AA1 4 PHE A 239 ILE A 241 0 SHEET 2 AA1 4 GLY A 337 THR A 340 1 O PHE A 338 N ILE A 241 SHEET 3 AA1 4 GLY A 329 VAL A 332 -1 N MET A 330 O ILE A 339 SHEET 4 AA1 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 4.01 SITE 1 AC1 16 LEU A 247 PHE A 273 CYS A 276 THR A 279 SITE 2 AC1 16 SER A 280 TYR A 314 MET A 330 VAL A 332 SITE 3 AC1 16 ALA A 333 ILE A 339 ILE A 354 MET A 355 SITE 4 AC1 16 LYS A 358 HIS A 440 TYR A 464 HOH A 614 CRYST1 44.841 61.803 53.134 90.00 106.16 90.00 P 1 21 1 2 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 0.022301 0.000000 0.006463 0.00000 SCALE2 0.000000 0.016180 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019595 0.00000