HEADER TRANSCRIPTION 10-NOV-09 3KMG TITLE THE X-RAY CRYSTAL STRUCTURE OF PPAR-GAMMA IN COMPLEX WITH AN INDOLE TITLE 2 DERIVATIVE MODULATOR, GSK538, AND AN SRC-1 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 234-505; COMPND 5 SYNONYM: PPAR-GAMMA, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C MEMBER 3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: STEROID RECEPTOR COACTIVATOR-1; COMPND 9 CHAIN: B, E; 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 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PRSETA; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHETIC PEPTIDE COMPOUND KEYWDS PPAR-GAMMA, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR, TELMISARTAN, KEYWDS 2 DIABETES, MODULATOR, ACTIVATOR, DIABETES MELLITUS, DISEASE MUTATION, KEYWDS 3 DNA-BINDING, METAL-BINDING, NUCLEUS, OBESITY, PHOSPHOPROTEIN, KEYWDS 4 RECEPTOR, TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR R.GAMPE REVDAT 6 13-MAR-24 3KMG 1 COMPND SOURCE REVDAT 5 06-SEP-23 3KMG 1 REMARK REVDAT 4 24-JAN-18 3KMG 1 JRNL REVDAT 3 01-NOV-17 3KMG 1 REMARK REVDAT 2 13-JUL-11 3KMG 1 VERSN REVDAT 1 12-JAN-10 3KMG 0 JRNL AUTH Y.LAMOTTE,P.MARTRES,N.FAUCHER,A.LAROZE,D.GRILLOT,N.ANCELLIN, JRNL AUTH 2 Y.SAINTILLAN,V.BENETON,R.GAMPE JRNL TITL SYNTHESIS AND BIOLOGICAL ACTIVITIES OF NOVEL INDOLE JRNL TITL 2 DERIVATIVES AS POTENT AND SELECTIVE PPAR-GAMMA MODULATORS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 38828 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1247 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2759 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4239 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.01000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.199 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.395 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4453 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2986 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6030 ; 1.256 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7344 ; 0.887 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 557 ; 6.002 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;34.952 ;24.919 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 810 ;13.985 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.365 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 699 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4873 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 864 ; 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): 2735 ; 0.490 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1098 ; 0.090 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4410 ; 0.922 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1718 ; 1.425 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1610 ; 2.320 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 209 A 476 REMARK 3 RESIDUE RANGE : B 686 B 695 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4360 25.5230 5.3160 REMARK 3 T TENSOR REMARK 3 T11: -0.1962 T22: -0.2189 REMARK 3 T33: -0.1212 T12: -0.0051 REMARK 3 T13: 0.0409 T23: 0.0036 REMARK 3 L TENSOR REMARK 3 L11: 2.2258 L22: 1.5120 REMARK 3 L33: 3.8502 L12: 0.0541 REMARK 3 L13: 0.7725 L23: -0.6868 REMARK 3 S TENSOR REMARK 3 S11: 0.0607 S12: -0.0343 S13: -0.0007 REMARK 3 S21: 0.0383 S22: -0.1397 S23: -0.1284 REMARK 3 S31: 0.0589 S32: 0.1002 S33: 0.0790 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 : D 208 D 476 REMARK 3 RESIDUE RANGE : E 682 E 698 REMARK 3 ORIGIN FOR THE GROUP (A): 1.4290 55.6370 -2.7550 REMARK 3 T TENSOR REMARK 3 T11: -0.0746 T22: -0.1474 REMARK 3 T33: -0.1354 T12: 0.0188 REMARK 3 T13: 0.0147 T23: -0.0609 REMARK 3 L TENSOR REMARK 3 L11: 2.6083 L22: 2.3161 REMARK 3 L33: 2.3635 L12: 0.5285 REMARK 3 L13: -0.8932 L23: 0.1117 REMARK 3 S TENSOR REMARK 3 S11: -0.0197 S12: -0.2334 S13: 0.1654 REMARK 3 S21: 0.1811 S22: 0.0105 S23: 0.1434 REMARK 3 S31: -0.2018 S32: 0.2464 S33: 0.0093 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK 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 3KMG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056174. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUL-06 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 : 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 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39982 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.03800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.8 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.42700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: RCSB ENTRY 1FM9 CHAIN D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DIFFRACTION GRADE CRYSTALS GREW IN 7 REMARK 280 -14 DAYS AT 22C USING 2UL VAPOR DIFFUSED HANGING DROPS MADE WITH REMARK 280 1UL OF THE COMPLEX AND 1UL OF THE WELL SOLUTION COMPRISED OF 14% REMARK 280 PEG4K, 0.2M NASCN AND 0.1M BIS-TRIS PH 6.5., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 295K 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 41.66750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.21250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.07900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.21250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.66750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.07900 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12890 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 PRO A 206 REMARK 465 GLU A 207 REMARK 465 SER A 208 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 ASP A 462 REMARK 465 TYR A 477 REMARK 465 ACE B 675 REMARK 465 CYS B 676 REMARK 465 PRO B 677 REMARK 465 SER B 678 REMARK 465 SER B 679 REMARK 465 HIS B 680 REMARK 465 SER B 681 REMARK 465 SER B 682 REMARK 465 LEU B 683 REMARK 465 THR B 684 REMARK 465 GLU B 696 REMARK 465 GLY B 697 REMARK 465 SER B 698 REMARK 465 PRO B 699 REMARK 465 SER B 700 REMARK 465 NH2 B 701 REMARK 465 PRO D 206 REMARK 465 GLU D 207 REMARK 465 ILE D 262 REMARK 465 LYS D 263 REMARK 465 PHE D 264 REMARK 465 LYS D 265 REMARK 465 HIS D 266 REMARK 465 ILE D 267 REMARK 465 THR D 268 REMARK 465 PRO D 269 REMARK 465 LEU D 270 REMARK 465 GLN D 271 REMARK 465 GLU D 272 REMARK 465 GLN D 273 REMARK 465 SER D 274 REMARK 465 TYR D 477 REMARK 465 ACE E 675 REMARK 465 CYS E 676 REMARK 465 PRO E 677 REMARK 465 SER E 678 REMARK 465 SER E 679 REMARK 465 HIS E 680 REMARK 465 SER E 681 REMARK 465 SER E 700 REMARK 465 NH2 E 701 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 224 CG CD CE NZ REMARK 470 LYS A 232 CD CE NZ REMARK 470 LYS A 240 CD CE NZ REMARK 470 THR A 242 CB OG1 CG2 REMARK 470 ASP A 243 CB CG OD1 OD2 REMARK 470 LYS A 244 CG CD CE NZ REMARK 470 ILE A 262 CG1 CG2 CD1 REMARK 470 GLU A 272 CG CD OE1 OE2 REMARK 470 GLU A 343 CG CD OE1 OE2 REMARK 470 LYS A 358 CD CE NZ REMARK 470 LYS A 434 CE NZ REMARK 470 GLN A 451 OE1 NE2 REMARK 470 LEU A 452 CD1 CD2 REMARK 470 LYS A 457 CG CD CE NZ REMARK 470 LYS A 458 CE NZ REMARK 470 THR A 461 CB OG1 CG2 REMARK 470 MET A 463 CB CG SD CE REMARK 470 SER A 464 CB OG REMARK 470 LYS A 474 CD CE NZ REMARK 470 GLU B 685 CG CD OE1 OE2 REMARK 470 ARG B 686 CD NE CZ NH1 NH2 REMARK 470 LYS D 240 CD CE NZ REMARK 470 ASP D 243 CG OD1 OD2 REMARK 470 LYS D 244 CD CE NZ REMARK 470 LYS D 261 CG CD CE NZ REMARK 470 VAL D 277 CG1 CG2 REMARK 470 GLU D 298 CD OE1 OE2 REMARK 470 LYS D 358 CD CE NZ REMARK 470 LYS D 404 CD CE NZ REMARK 470 LYS D 422 CD CE NZ REMARK 470 GLU D 427 CD OE1 OE2 REMARK 470 GLN D 451 CD OE1 NE2 REMARK 470 VAL D 455 CG1 CG2 REMARK 470 LYS D 457 CG CD CE NZ REMARK 470 LYS D 458 CD CE NZ REMARK 470 GLU D 460 CG CD OE1 OE2 REMARK 470 ASP D 462 CG OD1 OD2 REMARK 470 MET D 463 SD CE REMARK 470 SER D 464 OG REMARK 470 LYS D 474 CE NZ REMARK 470 LEU D 476 CG CD1 CD2 REMARK 470 ARG E 686 NE CZ NH1 NH2 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 CD1 ILE A 326 O HOH A 42 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 326 CG1 - CB - CG2 ANGL. DEV. = -18.5 DEGREES REMARK 500 THR E 684 N - CA - C ANGL. DEV. = 16.7 DEGREES 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 48.25 -93.61 REMARK 500 THR A 242 39.22 91.70 REMARK 500 ASP A 243 -151.18 -79.36 REMARK 500 ALA D 209 -81.18 87.31 REMARK 500 LYS D 457 46.75 -67.04 REMARK 500 LYS D 458 -89.26 -137.16 REMARK 500 THR D 461 48.38 -96.81 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU E 683 THR E 684 74.45 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 538 A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 538 D 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PRG RELATED DB: PDB REMARK 900 LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR REMARK 900 ACTIVATED RECEPTOR GAMMA REMARK 900 RELATED ID: 1FM6 RELATED DB: PDB REMARK 900 THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF REMARK 900 THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS REMARK 900 RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND ROSIGLITAZONE AND REMARK 900 CO-ACTIVATOR PEPTIDES. REMARK 900 RELATED ID: 1FM9 RELATED DB: PDB REMARK 900 THE 2.1 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE HETERODIMER OF REMARK 900 THE HUMAN RXRALPHA AND PPARGAMMA LIGAND BINDING DOMAINS REMARK 900 RESPECTIVELY BOUND WITH 9-CIS RETINOIC ACID AND GI262570 AND CO- REMARK 900 ACTIVATOR PEPTIDES. REMARK 900 RELATED ID: 1PRG RELATED DB: PDB REMARK 900 LIGAND-BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR REMARK 900 ACTIVATED RECEPTOR GAMMA DBREF 3KMG A 206 477 UNP P37231 PPARG_HUMAN 234 505 DBREF 3KMG D 206 477 UNP P37231 PPARG_HUMAN 234 505 DBREF 3KMG B 675 701 PDB 3KMG 3KMG 675 701 DBREF 3KMG E 675 701 PDB 3KMG 3KMG 675 701 SEQRES 1 A 272 PRO GLU SER ALA ASP LEU ARG ALA LEU ALA LYS HIS LEU SEQRES 2 A 272 TYR ASP SER TYR ILE LYS SER PHE PRO LEU THR LYS ALA SEQRES 3 A 272 LYS ALA ARG ALA ILE LEU THR GLY LYS THR THR ASP LYS SEQRES 4 A 272 SER PRO PHE VAL ILE TYR ASP MET ASN SER LEU MET MET SEQRES 5 A 272 GLY GLU ASP LYS ILE LYS PHE LYS HIS ILE THR PRO LEU SEQRES 6 A 272 GLN GLU GLN SER LYS GLU VAL ALA ILE ARG ILE PHE GLN SEQRES 7 A 272 GLY CYS GLN PHE ARG SER VAL GLU ALA VAL GLN GLU ILE SEQRES 8 A 272 THR GLU TYR ALA LYS SER ILE PRO GLY PHE VAL ASN LEU SEQRES 9 A 272 ASP LEU ASN ASP GLN VAL THR LEU LEU LYS TYR GLY VAL SEQRES 10 A 272 HIS GLU ILE ILE TYR THR MET LEU ALA SER LEU MET ASN SEQRES 11 A 272 LYS ASP GLY VAL LEU ILE SER GLU GLY GLN GLY PHE MET SEQRES 12 A 272 THR ARG GLU PHE LEU LYS SER LEU ARG LYS PRO PHE GLY SEQRES 13 A 272 ASP PHE MET GLU PRO LYS PHE GLU PHE ALA VAL LYS PHE SEQRES 14 A 272 ASN ALA LEU GLU LEU ASP ASP SER ASP LEU ALA ILE PHE SEQRES 15 A 272 ILE ALA VAL ILE ILE LEU SER GLY ASP ARG PRO GLY LEU SEQRES 16 A 272 LEU ASN VAL LYS PRO ILE GLU ASP ILE GLN ASP ASN LEU SEQRES 17 A 272 LEU GLN ALA LEU GLU LEU GLN LEU LYS LEU ASN HIS PRO SEQRES 18 A 272 GLU SER SER GLN LEU PHE ALA LYS LEU LEU GLN LYS MET SEQRES 19 A 272 THR ASP LEU ARG GLN ILE VAL THR GLU HIS VAL GLN LEU SEQRES 20 A 272 LEU GLN VAL ILE LYS LYS THR GLU THR ASP MET SER LEU SEQRES 21 A 272 HIS PRO LEU LEU GLN GLU ILE TYR LYS ASP LEU TYR SEQRES 1 B 27 ACE CYS PRO SER SER HIS SER SER LEU THR GLU ARG HIS SEQRES 2 B 27 LYS ILE LEU HIS ARG LEU LEU GLN GLU GLY SER PRO SER SEQRES 3 B 27 NH2 SEQRES 1 D 272 PRO GLU SER ALA ASP LEU ARG ALA LEU ALA LYS HIS LEU SEQRES 2 D 272 TYR ASP SER TYR ILE LYS SER PHE PRO LEU THR LYS ALA SEQRES 3 D 272 LYS ALA ARG ALA ILE LEU THR GLY LYS THR THR ASP LYS SEQRES 4 D 272 SER PRO PHE VAL ILE TYR ASP MET ASN SER LEU MET MET SEQRES 5 D 272 GLY GLU ASP LYS ILE LYS PHE LYS HIS ILE THR PRO LEU SEQRES 6 D 272 GLN GLU GLN SER LYS GLU VAL ALA ILE ARG ILE PHE GLN SEQRES 7 D 272 GLY CYS GLN PHE ARG SER VAL GLU ALA VAL GLN GLU ILE SEQRES 8 D 272 THR GLU TYR ALA LYS SER ILE PRO GLY PHE VAL ASN LEU SEQRES 9 D 272 ASP LEU ASN ASP GLN VAL THR LEU LEU LYS TYR GLY VAL SEQRES 10 D 272 HIS GLU ILE ILE TYR THR MET LEU ALA SER LEU MET ASN SEQRES 11 D 272 LYS ASP GLY VAL LEU ILE SER GLU GLY GLN GLY PHE MET SEQRES 12 D 272 THR ARG GLU PHE LEU LYS SER LEU ARG LYS PRO PHE GLY SEQRES 13 D 272 ASP PHE MET GLU PRO LYS PHE GLU PHE ALA VAL LYS PHE SEQRES 14 D 272 ASN ALA LEU GLU LEU ASP ASP SER ASP LEU ALA ILE PHE SEQRES 15 D 272 ILE ALA VAL ILE ILE LEU SER GLY ASP ARG PRO GLY LEU SEQRES 16 D 272 LEU ASN VAL LYS PRO ILE GLU ASP ILE GLN ASP ASN LEU SEQRES 17 D 272 LEU GLN ALA LEU GLU LEU GLN LEU LYS LEU ASN HIS PRO SEQRES 18 D 272 GLU SER SER GLN LEU PHE ALA LYS LEU LEU GLN LYS MET SEQRES 19 D 272 THR ASP LEU ARG GLN ILE VAL THR GLU HIS VAL GLN LEU SEQRES 20 D 272 LEU GLN VAL ILE LYS LYS THR GLU THR ASP MET SER LEU SEQRES 21 D 272 HIS PRO LEU LEU GLN GLU ILE TYR LYS ASP LEU TYR SEQRES 1 E 27 ACE CYS PRO SER SER HIS SER SER LEU THR GLU ARG HIS SEQRES 2 E 27 LYS ILE LEU HIS ARG LEU LEU GLN GLU GLY SER PRO SER SEQRES 3 E 27 NH2 HET 538 A 1 39 HET 538 D 1 39 HETNAM 538 4'-[(2,3-DIMETHYL-5-{[(1S)-1-PHENYLPROPYL]CARBAMOYL}- HETNAM 2 538 1H-INDOL-1-YL)METHYL]BIPHENYL-2-CARBOXYLIC ACID FORMUL 5 538 2(C34 H32 N2 O3) FORMUL 7 HOH *204(H2 O) HELIX 1 1 ASP A 210 PHE A 226 1 17 HELIX 2 2 THR A 229 THR A 238 1 10 HELIX 3 3 ASP A 251 LYS A 261 1 11 HELIX 4 4 GLU A 276 SER A 302 1 27 HELIX 5 5 GLY A 305 LEU A 309 5 5 HELIX 6 6 ASP A 310 ALA A 331 1 22 HELIX 7 7 SER A 342 GLY A 344 5 3 HELIX 8 8 ARG A 350 SER A 355 1 6 HELIX 9 9 PRO A 359 PHE A 363 5 5 HELIX 10 10 MET A 364 ALA A 376 1 13 HELIX 11 11 ASP A 380 LEU A 393 1 14 HELIX 12 12 ASN A 402 HIS A 425 1 24 HELIX 13 13 GLN A 430 GLN A 437 1 8 HELIX 14 14 LYS A 438 GLU A 460 1 23 HELIX 15 15 HIS A 466 LYS A 474 1 9 HELIX 16 16 HIS B 687 GLN B 695 1 9 HELIX 17 17 ALA D 209 PHE D 226 1 18 HELIX 18 18 THR D 229 THR D 238 1 10 HELIX 19 19 ASP D 251 ASP D 260 1 10 HELIX 20 20 GLU D 276 LYS D 301 1 26 HELIX 21 21 GLY D 305 LEU D 309 5 5 HELIX 22 22 ASP D 310 ALA D 331 1 22 HELIX 23 23 ARG D 350 LEU D 356 1 7 HELIX 24 24 PRO D 359 PHE D 363 5 5 HELIX 25 25 MET D 364 ALA D 376 1 13 HELIX 26 26 ASP D 380 LEU D 393 1 14 HELIX 27 27 ASN D 402 HIS D 425 1 24 HELIX 28 28 GLN D 430 LYS D 457 1 28 HELIX 29 29 HIS D 466 LYS D 474 1 9 HELIX 30 30 HIS E 687 GLY E 697 1 11 SHEET 1 A 4 PHE A 247 ILE A 249 0 SHEET 2 A 4 GLY A 346 THR A 349 1 O PHE A 347 N ILE A 249 SHEET 3 A 4 GLY A 338 ILE A 341 -1 N VAL A 339 O MET A 348 SHEET 4 A 4 MET A 334 ASN A 335 -1 N ASN A 335 O GLY A 338 SHEET 1 B 4 PHE D 247 ILE D 249 0 SHEET 2 B 4 GLY D 346 THR D 349 1 O PHE D 347 N ILE D 249 SHEET 3 B 4 GLY D 338 ILE D 341 -1 N VAL D 339 O MET D 348 SHEET 4 B 4 MET D 334 ASN D 335 -1 N ASN D 335 O GLY D 338 CISPEP 1 THR A 241 THR A 242 0 17.88 CISPEP 2 ASP A 243 LYS A 244 0 -5.66 CISPEP 3 LYS A 261 ILE A 262 0 3.49 CISPEP 4 LYS A 358 PRO A 359 0 1.85 CISPEP 5 SER D 208 ALA D 209 0 -20.75 CISPEP 6 LYS D 358 PRO D 359 0 1.00 CISPEP 7 THR D 459 GLU D 460 0 -1.07 CISPEP 8 GLU D 460 THR D 461 0 15.44 SITE 1 AC1 17 ARG A 280 PHE A 282 GLY A 284 CYS A 285 SITE 2 AC1 17 GLN A 286 ARG A 288 SER A 289 HIS A 323 SITE 3 AC1 17 ILE A 326 TYR A 327 LEU A 330 ILE A 341 SITE 4 AC1 17 SER A 342 PHE A 363 MET A 364 HIS A 449 SITE 5 AC1 17 TYR A 473 SITE 1 AC2 16 PHE D 282 GLY D 284 CYS D 285 GLN D 286 SITE 2 AC2 16 ARG D 288 SER D 289 HIS D 323 ILE D 326 SITE 3 AC2 16 TYR D 327 LEU D 330 ILE D 341 SER D 342 SITE 4 AC2 16 PHE D 363 MET D 364 HIS D 449 TYR D 473 CRYST1 83.335 84.158 96.425 90.00 90.00 90.00 P 21 21 21 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 0.012000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010371 0.00000