HEADER NUCLEAR PROTEIN 07-MAY-19 6K0T TITLE CRYSTAL STRUCTURE OF PPARGAMMA LIGAND BINDING DOMAIN IN COMPLEX WITH TITLE 2 DIBENZOOXEPINE DERIVATIVE COMPOUND-17 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: PPAR-GAMMA,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA COMPND 8 COACTIVATOR 1-ALPHA; COMPND 9 CHAIN: B, D; COMPND 10 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, NR1C3; 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 PPARGAMMA, LIGAND BINDING DOMAIN, PPARG MODULATOR, CANCER, NUCLEAR KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SUZUKI,K.YAMAMOTO,Y.TAKAHASHI,J.SAITO REVDAT 3 06-NOV-24 6K0T 1 REMARK REVDAT 2 06-NOV-19 6K0T 1 JRNL REVDAT 1 30-OCT-19 6K0T 0 JRNL AUTH K.YAMAMOTO,T.TAMURA,R.NAKAMURA,S.HOSOE,M.MATSUBARA,K.NAGATA, JRNL AUTH 2 H.KODAIRA,T.UEMORI,Y.TAKAHASHI,M.SUZUKI,J.I.SAITO,K.UENO, JRNL AUTH 3 S.SHUTO JRNL TITL DEVELOPMENT OF A NOVEL CLASS OF PEROXISOME JRNL TITL 2 PROLIFERATOR-ACTIVATED RECEPTOR (PPAR) GAMMA LIGANDS AS AN JRNL TITL 3 ANTICANCER AGENT WITH A UNIQUE BINDING MODE BASED ON A JRNL TITL 4 NON-THIAZOLIDINEDIONE SCAFFOLD. JRNL REF BIOORG.MED.CHEM. V. 27 15122 2019 JRNL REFN ESSN 1464-3391 JRNL PMID 31623970 JRNL DOI 10.1016/J.BMC.2019.115122 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0232 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 50181 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 + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2650 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3654 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3490 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.3930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4419 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 449 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.27 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : -0.75000 REMARK 3 B33 (A**2) : 0.76000 REMARK 3 B12 (A**2) : 0.02000 REMARK 3 B13 (A**2) : 0.84000 REMARK 3 B23 (A**2) : -0.25000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.136 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.200 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4646 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4518 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6287 ; 1.582 ; 1.669 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10537 ; 1.323 ; 1.591 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 5.978 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;35.074 ;24.206 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 897 ;17.266 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;17.645 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 608 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5027 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 870 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2220 ; 1.050 ; 1.794 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2219 ; 1.050 ; 1.794 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2770 ; 1.822 ; 2.674 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2771 ; 1.822 ; 2.674 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2426 ; 1.099 ; 1.948 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2426 ; 1.098 ; 1.948 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3500 ; 1.845 ; 2.873 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5563 ; 5.597 ;22.589 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5446 ; 5.467 ;21.909 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 205 A 477 REMARK 3 RESIDUE RANGE : B 141 B 150 REMARK 3 ORIGIN FOR THE GROUP (A): -8.6540 13.3060 12.7530 REMARK 3 T TENSOR REMARK 3 T11: 0.1363 T22: 0.1074 REMARK 3 T33: 0.0081 T12: -0.0374 REMARK 3 T13: -0.0136 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 1.9523 L22: 3.2557 REMARK 3 L33: 1.6755 L12: 0.0863 REMARK 3 L13: 0.4728 L23: -0.4488 REMARK 3 S TENSOR REMARK 3 S11: 0.0688 S12: -0.3151 S13: 0.0470 REMARK 3 S21: 0.6371 S22: -0.0251 S23: -0.1062 REMARK 3 S31: -0.1988 S32: 0.2157 S33: -0.0436 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 205 C 477 REMARK 3 RESIDUE RANGE : D 139 D 150 REMARK 3 ORIGIN FOR THE GROUP (A): 8.5610 40.1930 -13.5930 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.0963 REMARK 3 T33: 0.0106 T12: 0.0647 REMARK 3 T13: -0.0219 T23: 0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.8841 L22: 3.2611 REMARK 3 L33: 1.9316 L12: -0.3516 REMARK 3 L13: 0.3598 L23: 0.5322 REMARK 3 S TENSOR REMARK 3 S11: 0.1135 S12: 0.3049 S13: 0.0778 REMARK 3 S21: -0.6843 S22: -0.1261 S23: 0.1278 REMARK 3 S31: -0.3011 S32: -0.2368 S33: 0.0125 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6K0T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300011935. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52839 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 43.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M MAGNESIUM ACETATE, 0.1M SODIUM REMARK 280 ACETATE, 12% PEG 8,000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 191 REMARK 465 SER A 192 REMARK 465 HIS A 193 REMARK 465 MET A 194 REMARK 465 ALA A 195 REMARK 465 GLU A 196 REMARK 465 ILE A 197 REMARK 465 SER A 198 REMARK 465 SER A 199 REMARK 465 ASP A 200 REMARK 465 ILE A 201 REMARK 465 ASP A 202 REMARK 465 GLN A 203 REMARK 465 LEU A 204 REMARK 465 LYS A 263 REMARK 465 PHE A 264 REMARK 465 LYS A 265 REMARK 465 HIS A 266 REMARK 465 ILE A 267 REMARK 465 THR A 268 REMARK 465 PRO A 269 REMARK 465 LEU A 270 REMARK 465 GLN A 271 REMARK 465 GLU A 272 REMARK 465 GLN A 273 REMARK 465 SER A 274 REMARK 465 GLU B 139 REMARK 465 GLU B 140 REMARK 465 GLY C 191 REMARK 465 SER C 192 REMARK 465 HIS C 193 REMARK 465 MET C 194 REMARK 465 ALA C 195 REMARK 465 GLU C 196 REMARK 465 ILE C 197 REMARK 465 SER C 198 REMARK 465 SER C 199 REMARK 465 ASP C 200 REMARK 465 ILE C 201 REMARK 465 ASP C 202 REMARK 465 GLN C 203 REMARK 465 LEU C 204 REMARK 465 LEU C 270 REMARK 465 GLN C 271 REMARK 465 GLU C 272 REMARK 465 GLN C 273 REMARK 465 SER C 274 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 275 CG CD CE NZ 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 OE2 GLU A 407 O HOH A 601 2.11 REMARK 500 OE1 GLU A 298 O HOH A 602 2.13 REMARK 500 O HOH A 714 O HOH A 770 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OH TYR A 250 O LYS C 263 1556 2.17 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 LYS A 240 35.29 -95.97 REMARK 500 GLU A 276 134.49 -30.04 REMARK 500 ASP A 310 125.76 -39.02 REMARK 500 GLU A 343 29.24 49.03 REMARK 500 ASP A 475 -10.41 82.27 REMARK 500 ASP C 243 174.56 -52.44 REMARK 500 ASP C 310 132.83 -38.31 REMARK 500 LEU C 393 46.52 -91.10 REMARK 500 ASP C 462 53.15 -99.89 REMARK 500 ASP C 475 -9.20 80.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 829 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 830 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 831 DISTANCE = 7.22 ANGSTROMS REMARK 525 HOH C 810 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH C 811 DISTANCE = 5.90 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CTU A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CTU C 501 DBREF 6K0T A 195 477 UNP P37231 PPARG_HUMAN 223 505 DBREF 6K0T B 139 150 PDB 6K0T 6K0T 139 150 DBREF 6K0T C 195 477 UNP P37231 PPARG_HUMAN 223 505 DBREF 6K0T D 139 150 PDB 6K0T 6K0T 139 150 SEQADV 6K0T GLY A 191 UNP P37231 EXPRESSION TAG SEQADV 6K0T SER A 192 UNP P37231 EXPRESSION TAG SEQADV 6K0T HIS A 193 UNP P37231 EXPRESSION TAG SEQADV 6K0T MET A 194 UNP P37231 EXPRESSION TAG SEQADV 6K0T GLY C 191 UNP P37231 EXPRESSION TAG SEQADV 6K0T SER C 192 UNP P37231 EXPRESSION TAG SEQADV 6K0T HIS C 193 UNP P37231 EXPRESSION TAG SEQADV 6K0T MET C 194 UNP P37231 EXPRESSION TAG SEQRES 1 A 287 GLY SER HIS MET ALA GLU ILE SER SER ASP ILE ASP GLN SEQRES 2 A 287 LEU ASN PRO GLU SER ALA ASP LEU ARG ALA LEU ALA LYS SEQRES 3 A 287 HIS LEU TYR ASP SER TYR ILE LYS SER PHE PRO LEU THR SEQRES 4 A 287 LYS ALA LYS ALA ARG ALA ILE LEU THR GLY LYS THR THR SEQRES 5 A 287 ASP LYS SER PRO PHE VAL ILE TYR ASP MET ASN SER LEU SEQRES 6 A 287 MET MET GLY GLU ASP LYS ILE LYS PHE LYS HIS ILE THR SEQRES 7 A 287 PRO LEU GLN GLU GLN SER LYS GLU VAL ALA ILE ARG ILE SEQRES 8 A 287 PHE GLN GLY CME GLN PHE ARG SER VAL GLU ALA VAL GLN SEQRES 9 A 287 GLU ILE THR GLU TYR ALA LYS SER ILE PRO GLY PHE VAL SEQRES 10 A 287 ASN LEU ASP LEU ASN ASP GLN VAL THR LEU LEU LYS TYR SEQRES 11 A 287 GLY VAL HIS GLU ILE ILE TYR THR MET LEU ALA SER LEU SEQRES 12 A 287 MET ASN LYS ASP GLY VAL LEU ILE SER GLU GLY GLN GLY SEQRES 13 A 287 PHE MET THR ARG GLU PHE LEU LYS SER LEU ARG LYS PRO SEQRES 14 A 287 PHE GLY ASP PHE MET GLU PRO LYS PHE GLU PHE ALA VAL SEQRES 15 A 287 LYS PHE ASN ALA LEU GLU LEU ASP ASP SER ASP LEU ALA SEQRES 16 A 287 ILE PHE ILE ALA VAL ILE ILE LEU SER GLY ASP ARG PRO SEQRES 17 A 287 GLY LEU LEU ASN VAL LYS PRO ILE GLU ASP ILE GLN ASP SEQRES 18 A 287 ASN LEU LEU GLN ALA LEU GLU LEU GLN LEU LYS LEU ASN SEQRES 19 A 287 HIS PRO GLU SER SER GLN LEU PHE ALA LYS LEU LEU GLN SEQRES 20 A 287 LYS MET THR ASP LEU ARG GLN ILE VAL THR GLU HIS VAL SEQRES 21 A 287 GLN LEU LEU GLN VAL ILE LYS LYS THR GLU THR ASP MET SEQRES 22 A 287 SER LEU HIS PRO LEU LEU GLN GLU ILE TYR LYS ASP LEU SEQRES 23 A 287 TYR SEQRES 1 B 12 GLU GLU PRO SER LEU LEU LYS LYS LEU LEU LEU ALA SEQRES 1 C 287 GLY SER HIS MET ALA GLU ILE SER SER ASP ILE ASP GLN SEQRES 2 C 287 LEU ASN PRO GLU SER ALA ASP LEU ARG ALA LEU ALA LYS SEQRES 3 C 287 HIS LEU TYR ASP SER TYR ILE LYS SER PHE PRO LEU THR SEQRES 4 C 287 LYS ALA LYS ALA ARG ALA ILE LEU THR GLY LYS THR THR SEQRES 5 C 287 ASP LYS SER PRO PHE VAL ILE TYR ASP MET ASN SER LEU SEQRES 6 C 287 MET MET GLY GLU ASP LYS ILE LYS PHE LYS HIS ILE THR SEQRES 7 C 287 PRO LEU GLN GLU GLN SER LYS GLU VAL ALA ILE ARG ILE SEQRES 8 C 287 PHE GLN GLY CME GLN PHE ARG SER VAL GLU ALA VAL GLN SEQRES 9 C 287 GLU ILE THR GLU TYR ALA LYS SER ILE PRO GLY PHE VAL SEQRES 10 C 287 ASN LEU ASP LEU ASN ASP GLN VAL THR LEU LEU LYS TYR SEQRES 11 C 287 GLY VAL HIS GLU ILE ILE TYR THR MET LEU ALA SER LEU SEQRES 12 C 287 MET ASN LYS ASP GLY VAL LEU ILE SER GLU GLY GLN GLY SEQRES 13 C 287 PHE MET THR ARG GLU PHE LEU LYS SER LEU ARG LYS PRO SEQRES 14 C 287 PHE GLY ASP PHE MET GLU PRO LYS PHE GLU PHE ALA VAL SEQRES 15 C 287 LYS PHE ASN ALA LEU GLU LEU ASP ASP SER ASP LEU ALA SEQRES 16 C 287 ILE PHE ILE ALA VAL ILE ILE LEU SER GLY ASP ARG PRO SEQRES 17 C 287 GLY LEU LEU ASN VAL LYS PRO ILE GLU ASP ILE GLN ASP SEQRES 18 C 287 ASN LEU LEU GLN ALA LEU GLU LEU GLN LEU LYS LEU ASN SEQRES 19 C 287 HIS PRO GLU SER SER GLN LEU PHE ALA LYS LEU LEU GLN SEQRES 20 C 287 LYS MET THR ASP LEU ARG GLN ILE VAL THR GLU HIS VAL SEQRES 21 C 287 GLN LEU LEU GLN VAL ILE LYS LYS THR GLU THR ASP MET SEQRES 22 C 287 SER LEU HIS PRO LEU LEU GLN GLU ILE TYR LYS ASP LEU SEQRES 23 C 287 TYR SEQRES 1 D 12 GLU GLU PRO SER LEU LEU LYS LYS LEU LEU LEU ALA MODRES 6K0T CME A 285 CYS MODIFIED RESIDUE MODRES 6K0T CME C 285 CYS MODIFIED RESIDUE HET CME A 285 10 HET CME C 285 10 HET CTU A 501 38 HET CTU C 501 38 HETNAM CME S,S-(2-HYDROXYETHYL)THIOCYSTEINE HETNAM CTU 3-[(1~{E})-1-[8-[(8-CHLORANYL-2-CYCLOPROPYL-IMIDAZO[1, HETNAM 2 CTU 2-A]PYRIDIN-3-YL)METHYL]-3-FLUORANYL-6~{H}- HETNAM 3 CTU BENZO[C][1]BENZOXEPIN-11-YLIDENE]ETHYL]-4~{H}-1,2,4- HETNAM 4 CTU OXADIAZOL-5-ONE FORMUL 1 CME 2(C5 H11 N O3 S2) FORMUL 5 CTU 2(C29 H22 CL F N4 O3) FORMUL 7 HOH *449(H2 O) HELIX 1 AA1 GLU A 207 PHE A 226 1 20 HELIX 2 AA2 THR A 229 THR A 238 1 10 HELIX 3 AA3 ASP A 251 GLY A 258 1 8 HELIX 4 AA4 GLU A 259 ILE A 262 5 4 HELIX 5 AA5 GLU A 276 GLY A 284 1 9 HELIX 6 AA6 CME A 285 SER A 302 1 18 HELIX 7 AA7 GLY A 305 LEU A 309 5 5 HELIX 8 AA8 ASP A 310 SER A 332 1 23 HELIX 9 AA9 SER A 342 GLY A 344 5 3 HELIX 10 AB1 ARG A 350 SER A 355 1 6 HELIX 11 AB2 PRO A 359 MET A 364 1 6 HELIX 12 AB3 MET A 364 ALA A 376 1 13 HELIX 13 AB4 ASP A 380 LEU A 393 1 14 HELIX 14 AB5 ASN A 402 HIS A 425 1 24 HELIX 15 AB6 GLN A 430 LYS A 457 1 28 HELIX 16 AB7 HIS A 466 LYS A 474 1 9 HELIX 17 AB8 SER B 142 LEU B 149 1 8 HELIX 18 AB9 GLU C 207 PHE C 226 1 20 HELIX 19 AC1 THR C 229 THR C 238 1 10 HELIX 20 AC2 ASP C 251 GLU C 259 1 9 HELIX 21 AC3 ASP C 260 ILE C 262 5 3 HELIX 22 AC4 GLU C 276 GLY C 284 1 9 HELIX 23 AC5 CME C 285 SER C 302 1 18 HELIX 24 AC6 GLY C 305 LEU C 309 5 5 HELIX 25 AC7 ASP C 310 SER C 332 1 23 HELIX 26 AC8 SER C 342 GLY C 344 5 3 HELIX 27 AC9 ARG C 350 SER C 355 1 6 HELIX 28 AD1 PRO C 359 PHE C 363 5 5 HELIX 29 AD2 MET C 364 ALA C 376 1 13 HELIX 30 AD3 ASP C 380 LEU C 393 1 14 HELIX 31 AD4 ASN C 402 HIS C 425 1 24 HELIX 32 AD5 GLN C 430 LYS C 458 1 29 HELIX 33 AD6 HIS C 466 LYS C 474 1 9 HELIX 34 AD7 SER D 142 ALA D 150 1 9 SHEET 1 AA1 4 PHE A 247 ILE A 249 0 SHEET 2 AA1 4 GLY A 346 THR A 349 1 O PHE A 347 N ILE A 249 SHEET 3 AA1 4 GLY A 338 ILE A 341 -1 N VAL A 339 O MET A 348 SHEET 4 AA1 4 MET A 334 ASN A 335 -1 N ASN A 335 O GLY A 338 SHEET 1 AA2 4 PHE C 247 ILE C 249 0 SHEET 2 AA2 4 GLY C 346 THR C 349 1 O PHE C 347 N ILE C 249 SHEET 3 AA2 4 GLY C 338 ILE C 341 -1 N ILE C 341 O GLY C 346 SHEET 4 AA2 4 MET C 334 ASN C 335 -1 N ASN C 335 O GLY C 338 LINK C GLY A 284 N CME A 285 1555 1555 1.34 LINK C CME A 285 N GLN A 286 1555 1555 1.33 LINK C GLY C 284 N CME C 285 1555 1555 1.34 LINK C CME C 285 N GLN C 286 1555 1555 1.33 CISPEP 1 LYS A 358 PRO A 359 0 -2.63 CISPEP 2 LYS C 358 PRO C 359 0 3.86 SITE 1 AC1 17 PHE A 282 GLN A 283 CME A 285 SER A 289 SITE 2 AC1 17 HIS A 323 ILE A 326 TYR A 327 ILE A 341 SITE 3 AC1 17 PHE A 360 PHE A 363 MET A 364 HIS A 449 SITE 4 AC1 17 LEU A 452 ILE A 456 MET A 463 TYR A 473 SITE 5 AC1 17 HOH A 738 SITE 1 AC2 17 PHE C 282 GLN C 283 CME C 285 GLN C 286 SITE 2 AC2 17 SER C 289 HIS C 323 ILE C 326 TYR C 327 SITE 3 AC2 17 LEU C 353 PHE C 360 MET C 364 HIS C 449 SITE 4 AC2 17 LEU C 452 ILE C 456 MET C 463 TYR C 473 SITE 5 AC2 17 HOH C 730 CRYST1 44.340 54.060 70.490 94.26 103.94 89.95 P 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 0.022553 -0.000020 0.005613 0.00000 SCALE2 0.000000 0.018498 0.001416 0.00000 SCALE3 0.000000 0.000000 0.014660 0.00000