HEADER TRANSCRIPTION 16-NOV-22 8HHP TITLE CRYSTAL STRUCTURE OF PPARG-LBD COMPLEXED WITH THREE PARTIAL AGONISTS, TITLE 2 ONE NTZDPA AND TWO LT175 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA; COMPND 3 CHAIN: A; COMPND 4 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: PPARG; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PPARG-LBD, PARTIAL AGONISTS, NTZDPA, LT175, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR H.KOJIMA,T.ITOH REVDAT 2 22-MAY-24 8HHP 1 JRNL REVDAT 1 22-NOV-23 8HHP 0 JRNL AUTH H.KOJIMA,R.YANAGI,E.HIGUCHI,M.YOSHIZAWA,T.SHIMODAIRA, JRNL AUTH 2 M.KUMAGAI,T.KYOYA,M.SEKINE,D.EGAWA,N.OHASHI,H.ISHIDA, JRNL AUTH 3 K.YAMAMOTO,T.ITOH JRNL TITL COVALENT MODIFIER DISCOVERY USING HYDROGEN/DEUTERIUM JRNL TITL 2 EXCHANGE-MASS SPECTROMETRY. JRNL REF J.MED.CHEM. V. 66 4827 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 36994595 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01986 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 11586 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1158 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 48.5000 - 4.9000 0.97 1404 157 0.2094 0.2389 REMARK 3 2 4.9000 - 3.8900 0.98 1316 145 0.1668 0.2428 REMARK 3 3 3.8900 - 3.4000 0.99 1299 145 0.2086 0.2609 REMARK 3 4 3.4000 - 3.0900 0.99 1300 144 0.2337 0.3366 REMARK 3 5 3.0900 - 2.8700 0.99 1287 144 0.2459 0.3635 REMARK 3 6 2.8600 - 2.7000 0.99 1278 141 0.2424 0.3171 REMARK 3 7 2.7000 - 2.5600 0.99 1277 142 0.2453 0.3341 REMARK 3 8 2.5600 - 2.4500 0.99 1267 140 0.2302 0.3303 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) : 0.338 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.987 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.76 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 : 0.009 2219 REMARK 3 ANGLE : 1.254 2999 REMARK 3 CHIRALITY : 0.067 340 REMARK 3 PLANARITY : 0.006 381 REMARK 3 DIHEDRAL : 17.381 297 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 8HHP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033615. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11599 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 48.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.57 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 2VV3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 7.7, 0.75 M SODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 81.13000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 30.25000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 30.25000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 121.69500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 30.25000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 30.25000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.56500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 30.25000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.25000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 121.69500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 30.25000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.25000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.56500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 81.13000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL 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 GLY A 202 REMARK 465 ALA A 203 REMARK 465 LEU A 204 REMARK 465 ASN A 205 REMARK 465 PRO A 206 REMARK 465 THR A 241 REMARK 465 THR A 242 REMARK 465 ASP A 243 REMARK 465 LYS A 244 REMARK 465 LYS A 263 REMARK 465 PHE A 264 REMARK 465 LYS A 265 REMARK 465 HIS A 266 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 LYS A 319 CG CD CE NZ REMARK 470 LYS A 422 CG CD CE NZ REMARK 470 LYS A 457 CG CD CE NZ REMARK 470 LYS A 458 CG CD CE NZ REMARK 470 MET A 463 CG SD CE 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 NE2 GLN A 437 O HOH A 601 2.05 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 ASN A 335 -169.64 -127.31 REMARK 500 LEU A 393 52.14 -91.78 REMARK 500 THR A 461 -54.06 -123.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HHP A 204 477 UNP P37231 PPARG_HUMAN 204 477 SEQADV 8HHP GLY A 202 UNP P37231 EXPRESSION TAG SEQADV 8HHP ALA A 203 UNP P37231 EXPRESSION TAG SEQRES 1 A 276 GLY ALA LEU ASN PRO GLU SER ALA ASP LEU ARG ALA LEU SEQRES 2 A 276 ALA LYS HIS LEU TYR ASP SER TYR ILE LYS SER PHE PRO SEQRES 3 A 276 LEU THR LYS ALA LYS ALA ARG ALA ILE LEU THR GLY LYS SEQRES 4 A 276 THR THR ASP LYS SER PRO PHE VAL ILE TYR ASP MET ASN SEQRES 5 A 276 SER LEU MET MET GLY GLU ASP LYS ILE LYS PHE LYS HIS SEQRES 6 A 276 ILE THR PRO LEU GLN GLU GLN SER LYS GLU VAL ALA ILE SEQRES 7 A 276 ARG ILE PHE GLN GLY CYS GLN PHE ARG SER VAL GLU ALA SEQRES 8 A 276 VAL GLN GLU ILE THR GLU TYR ALA LYS SER ILE PRO GLY SEQRES 9 A 276 PHE VAL ASN LEU ASP LEU ASN ASP GLN VAL THR LEU LEU SEQRES 10 A 276 LYS TYR GLY VAL HIS GLU ILE ILE TYR THR MET LEU ALA SEQRES 11 A 276 SER LEU MET ASN LYS ASP GLY VAL LEU ILE SER GLU GLY SEQRES 12 A 276 GLN GLY PHE MET THR ARG GLU PHE LEU LYS SER LEU ARG SEQRES 13 A 276 LYS PRO PHE GLY ASP PHE MET GLU PRO LYS PHE GLU PHE SEQRES 14 A 276 ALA VAL LYS PHE ASN ALA LEU GLU LEU ASP ASP SER ASP SEQRES 15 A 276 LEU ALA ILE PHE ILE ALA VAL ILE ILE LEU SER GLY ASP SEQRES 16 A 276 ARG PRO GLY LEU LEU ASN VAL LYS PRO ILE GLU ASP ILE SEQRES 17 A 276 GLN ASP ASN LEU LEU GLN ALA LEU GLU LEU GLN LEU LYS SEQRES 18 A 276 LEU ASN HIS PRO GLU SER SER GLN LEU PHE ALA LYS LEU SEQRES 19 A 276 LEU GLN LYS MET THR ASP LEU ARG GLN ILE VAL THR GLU SEQRES 20 A 276 HIS VAL GLN LEU LEU GLN VAL ILE LYS LYS THR GLU THR SEQRES 21 A 276 ASP MET SER LEU HIS PRO LEU LEU GLN GLU ILE TYR LYS SEQRES 22 A 276 ASP LEU TYR HET NZA A 501 28 HET LRG A 502 24 HET LRG A 503 24 HETNAM NZA 5-CHLORO-1-(4-CHLOROBENZYL)-3-(PHENYLTHIO)-1H-INDOLE-2- HETNAM 2 NZA CARBOXYLIC ACID HETNAM LRG (2S)-2-(BIPHENYL-4-YLOXY)-3-PHENYLPROPANOIC ACID HETSYN NZA NTZDPA FORMUL 2 NZA C22 H15 CL2 N O2 S FORMUL 3 LRG 2(C21 H18 O3) FORMUL 5 HOH *33(H2 O) HELIX 1 AA1 GLU A 207 PHE A 226 1 20 HELIX 2 AA2 THR A 229 GLY A 239 1 11 HELIX 3 AA3 ASP A 251 LYS A 261 1 11 HELIX 4 AA4 PRO A 269 SER A 274 1 6 HELIX 5 AA5 GLU A 276 SER A 302 1 27 HELIX 6 AA6 GLY A 305 LEU A 309 5 5 HELIX 7 AA7 ASP A 310 SER A 332 1 23 HELIX 8 AA8 ARG A 350 SER A 355 1 6 HELIX 9 AA9 PRO A 359 PHE A 363 5 5 HELIX 10 AB1 MET A 364 ALA A 376 1 13 HELIX 11 AB2 ASP A 380 LEU A 393 1 14 HELIX 12 AB3 ASN A 402 HIS A 425 1 24 HELIX 13 AB4 GLN A 430 GLU A 460 1 31 HELIX 14 AB5 HIS A 466 TYR A 473 1 8 SHEET 1 AA1 3 PHE A 247 ILE A 249 0 SHEET 2 AA1 3 GLY A 346 THR A 349 1 O PHE A 347 N ILE A 249 SHEET 3 AA1 3 GLY A 338 ILE A 341 -1 N ILE A 341 O GLY A 346 CISPEP 1 LYS A 358 PRO A 359 0 5.38 CRYST1 60.500 60.500 162.260 90.00 90.00 90.00 P 43 21 2 8 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 0.016529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006163 0.00000