PDB Short entry for 3DY6 HEADER TRANSCRIPTION 25-JUL-08 3DY6 TITLE PPARDELTA COMPLEXED WITH AN ANTHRANILIC ACID PARTIAL AGONIST COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN RESIDUES 171-441; COMPND 5 SYNONYM: PPAR-DELTA, PPAR- BETA, NUCLEAR RECEPTOR SUBFAMILY 1 GROUP C COMPND 6 MEMBER 2, NUCLEAR HORMONE RECEPTOR 1, NUC1, NUCI; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: PPARD, NR1C2, PPARB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSETA KEYWDS PPAR, NULEAR RECEPTOR, ACTIVATOR, DNA-BINDING, METAL-BINDING, KEYWDS 2 NUCLEUS, TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR M.L.LAMBERT,R.XU,B.G.SHEARER,T.M.WILSON REVDAT 4 30-AUG-23 3DY6 1 REMARK REVDAT 3 13-JUL-11 3DY6 1 VERSN REVDAT 2 24-FEB-09 3DY6 1 VERSN REVDAT 1 07-OCT-08 3DY6 0 JRNL AUTH B.G.SHEARER,H.S.PATEL,A.N.BILLIN,J.M.WAY,D.A.WINEGAR, JRNL AUTH 2 M.H.LAMBERT,R.X.XU,L.M.LEESNITZER,R.V.MERRIHEW,S.HUET, JRNL AUTH 3 T.M.WILLSON JRNL TITL DISCOVERY OF A NOVEL CLASS OF PPARDELTA PARTIAL AGONISTS JRNL REF BIOORG.MED.CHEM.LETT. V. 18 5018 2008 JRNL REFN ISSN 0960-894X JRNL PMID 18722772 JRNL DOI 10.1016/J.BMCL.2008.08.011 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 14657 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 786 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 852 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4064 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 31 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) : 66.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.63000 REMARK 3 B22 (A**2) : 3.55000 REMARK 3 B33 (A**2) : -6.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.51000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.390 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.295 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 30.974 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4266 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5788 ; 1.048 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 516 ; 4.510 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;36.917 ;23.967 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 738 ;15.243 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;13.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 661 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3261 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1854 ; 0.197 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2996 ; 0.302 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 103 ; 0.145 ; 0.200 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): 44 ; 0.259 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.162 ; 0.200 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): 2597 ; 0.229 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4177 ; 0.414 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1802 ; 0.672 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1609 ; 1.173 ; 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 208 A 470 1 REMARK 3 1 B 210 B 470 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 1990 ; 0.04 ; 0.05 REMARK 3 TIGHT THERMAL 1 A (A**2): 1990 ; 0.08 ; 0.50 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 208 A 470 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5192 7.6363 66.2682 REMARK 3 T TENSOR REMARK 3 T11: -0.3465 T22: -0.2939 REMARK 3 T33: -0.1600 T12: -0.0412 REMARK 3 T13: -0.0226 T23: -0.0262 REMARK 3 L TENSOR REMARK 3 L11: 3.2281 L22: 2.4634 REMARK 3 L33: 6.0172 L12: -0.0061 REMARK 3 L13: -1.1973 L23: 0.6932 REMARK 3 S TENSOR REMARK 3 S11: -0.0424 S12: 0.2098 S13: -0.1459 REMARK 3 S21: 0.0289 S22: -0.0331 S23: 0.0050 REMARK 3 S31: 0.1247 S32: -0.2933 S33: 0.0755 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 210 B 470 REMARK 3 ORIGIN FOR THE GROUP (A): -0.0881 -0.5654 18.7414 REMARK 3 T TENSOR REMARK 3 T11: -0.0998 T22: -0.2172 REMARK 3 T33: -0.1341 T12: -0.0677 REMARK 3 T13: 0.0206 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 2.1708 L22: 2.5371 REMARK 3 L33: 7.7347 L12: 0.2474 REMARK 3 L13: -0.2546 L23: -1.4508 REMARK 3 S TENSOR REMARK 3 S11: 0.0570 S12: 0.1005 S13: 0.1605 REMARK 3 S21: 0.0247 S22: 0.0217 S23: 0.0833 REMARK 3 S31: -0.2441 S32: 0.2852 S33: -0.0787 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 3DY6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048636. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14657 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 96.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.25000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3GWX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM POTASSIUM IODIDE, PEG3500, PH REMARK 280 9.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 47.16200 REMARK 290 SMTRY3 2 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: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.6 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 25.87392 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 47.16200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 96.04931 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -39.88600 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 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 GLN A 207 REMARK 465 GLY A 239 REMARK 465 LYS A 240 REMARK 465 ALA A 241 REMARK 465 SER A 242 REMARK 465 HIS A 243 REMARK 465 THR A 244 REMARK 465 LYS A 265 REMARK 465 GLN A 266 REMARK 465 LEU A 267 REMARK 465 VAL A 268 REMARK 465 ASN A 269 REMARK 465 MET A 476 REMARK 465 TYR A 477 REMARK 465 GLN B 207 REMARK 465 VAL B 208 REMARK 465 ALA B 209 REMARK 465 GLY B 239 REMARK 465 LYS B 240 REMARK 465 ALA B 241 REMARK 465 SER B 242 REMARK 465 HIS B 243 REMARK 465 THR B 244 REMARK 465 LYS B 265 REMARK 465 GLN B 266 REMARK 465 LEU B 267 REMARK 465 VAL B 268 REMARK 465 ASN B 269 REMARK 465 MET B 476 REMARK 465 TYR B 477 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 ASP A 210 CG OD1 OD2 REMARK 470 LYS A 212 CG CD CE NZ REMARK 470 ARG A 234 NE CZ NH1 NH2 REMARK 470 GLU A 253 CG CD OE1 OE2 REMARK 470 LYS A 275 CG CD CE NZ REMARK 470 GLU A 291 CG CD OE1 OE2 REMARK 470 LYS A 336 CG CD CE NZ REMARK 470 GLN A 444 CD OE1 NE2 REMARK 470 ASP B 210 CG OD1 OD2 REMARK 470 LYS B 212 CG CD CE NZ REMARK 470 ARG B 234 NE CZ NH1 NH2 REMARK 470 LYS B 275 CG CD CE NZ REMARK 470 GLU B 291 CG CD OE1 OE2 REMARK 470 LYS B 336 CG CD CE NZ REMARK 470 GLU B 369 CD OE1 OE2 REMARK 470 PHE B 419 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 443 CG CD NE CZ NH1 NH2 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 260 0.96 -62.03 REMARK 500 LEU A 262 -7.74 -59.00 REMARK 500 VAL A 263 -39.73 -144.92 REMARK 500 ASN A 402 79.61 -110.25 REMARK 500 TYR A 430 17.45 55.28 REMARK 500 GLU A 460 63.14 -109.16 REMARK 500 LYS B 260 0.69 -61.55 REMARK 500 VAL B 263 -42.43 -143.03 REMARK 500 TYR B 430 18.87 54.78 REMARK 500 GLU B 460 62.31 -107.45 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 DY6 A 478 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DY6 B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GWX RELATED DB: PDB DBREF 3DY6 A 207 477 UNP Q03181 PPARD_HUMAN 171 441 DBREF 3DY6 B 207 477 UNP Q03181 PPARD_HUMAN 171 441 SEQRES 1 A 271 GLN VAL ALA ASP LEU LYS ALA PHE SER LYS HIS ILE TYR SEQRES 2 A 271 ASN ALA TYR LEU LYS ASN PHE ASN MET THR LYS LYS LYS SEQRES 3 A 271 ALA ARG SER ILE LEU THR GLY LYS ALA SER HIS THR ALA SEQRES 4 A 271 PRO PHE VAL ILE HIS ASP ILE GLU THR LEU TRP GLN ALA SEQRES 5 A 271 GLU LYS GLY LEU VAL TRP LYS GLN LEU VAL ASN GLY LEU SEQRES 6 A 271 PRO PRO TYR LYS GLU ILE SER VAL HIS VAL PHE TYR ARG SEQRES 7 A 271 CYS GLN CYS THR THR VAL GLU THR VAL ARG GLU LEU THR SEQRES 8 A 271 GLU PHE ALA LYS SER ILE PRO SER PHE SER SER LEU PHE SEQRES 9 A 271 LEU ASN ASP GLN VAL THR LEU LEU LYS TYR GLY VAL HIS SEQRES 10 A 271 GLU ALA ILE PHE ALA MET LEU ALA SER ILE VAL ASN LYS SEQRES 11 A 271 ASP GLY LEU LEU VAL ALA ASN GLY SER GLY PHE VAL THR SEQRES 12 A 271 ARG GLU PHE LEU ARG SER LEU ARG LYS PRO PHE SER ASP SEQRES 13 A 271 ILE ILE GLU PRO LYS PHE GLU PHE ALA VAL LYS PHE ASN SEQRES 14 A 271 ALA LEU GLU LEU ASP ASP SER ASP LEU ALA LEU PHE ILE SEQRES 15 A 271 ALA ALA ILE ILE LEU CYS GLY ASP ARG PRO GLY LEU MET SEQRES 16 A 271 ASN VAL PRO ARG VAL GLU ALA ILE GLN ASP THR ILE LEU SEQRES 17 A 271 ARG ALA LEU GLU PHE HIS LEU GLN ALA ASN HIS PRO ASP SEQRES 18 A 271 ALA GLN TYR LEU PHE PRO LYS LEU LEU GLN LYS MET ALA SEQRES 19 A 271 ASP LEU ARG GLN LEU VAL THR GLU HIS ALA GLN MET MET SEQRES 20 A 271 GLN ARG ILE LYS LYS THR GLU THR GLU THR SER LEU HIS SEQRES 21 A 271 PRO LEU LEU GLN GLU ILE TYR LYS ASP MET TYR SEQRES 1 B 271 GLN VAL ALA ASP LEU LYS ALA PHE SER LYS HIS ILE TYR SEQRES 2 B 271 ASN ALA TYR LEU LYS ASN PHE ASN MET THR LYS LYS LYS SEQRES 3 B 271 ALA ARG SER ILE LEU THR GLY LYS ALA SER HIS THR ALA SEQRES 4 B 271 PRO PHE VAL ILE HIS ASP ILE GLU THR LEU TRP GLN ALA SEQRES 5 B 271 GLU LYS GLY LEU VAL TRP LYS GLN LEU VAL ASN GLY LEU SEQRES 6 B 271 PRO PRO TYR LYS GLU ILE SER VAL HIS VAL PHE TYR ARG SEQRES 7 B 271 CYS GLN CYS THR THR VAL GLU THR VAL ARG GLU LEU THR SEQRES 8 B 271 GLU PHE ALA LYS SER ILE PRO SER PHE SER SER LEU PHE SEQRES 9 B 271 LEU ASN ASP GLN VAL THR LEU LEU LYS TYR GLY VAL HIS SEQRES 10 B 271 GLU ALA ILE PHE ALA MET LEU ALA SER ILE VAL ASN LYS SEQRES 11 B 271 ASP GLY LEU LEU VAL ALA ASN GLY SER GLY PHE VAL THR SEQRES 12 B 271 ARG GLU PHE LEU ARG SER LEU ARG LYS PRO PHE SER ASP SEQRES 13 B 271 ILE ILE GLU PRO LYS PHE GLU PHE ALA VAL LYS PHE ASN SEQRES 14 B 271 ALA LEU GLU LEU ASP ASP SER ASP LEU ALA LEU PHE ILE SEQRES 15 B 271 ALA ALA ILE ILE LEU CYS GLY ASP ARG PRO GLY LEU MET SEQRES 16 B 271 ASN VAL PRO ARG VAL GLU ALA ILE GLN ASP THR ILE LEU SEQRES 17 B 271 ARG ALA LEU GLU PHE HIS LEU GLN ALA ASN HIS PRO ASP SEQRES 18 B 271 ALA GLN TYR LEU PHE PRO LYS LEU LEU GLN LYS MET ALA SEQRES 19 B 271 ASP LEU ARG GLN LEU VAL THR GLU HIS ALA GLN MET MET SEQRES 20 B 271 GLN ARG ILE LYS LYS THR GLU THR GLU THR SER LEU HIS SEQRES 21 B 271 PRO LEU LEU GLN GLU ILE TYR LYS ASP MET TYR HET IOD A 1 1 HET DY6 A 478 31 HET DY6 B 1 31 HETNAM IOD IODIDE ION HETNAM DY6 2-({[3-(3,4-DIHYDROISOQUINOLIN-2(1H)-YLSULFONYL) HETNAM 2 DY6 PHENYL]CARBONYL}AMINO)BENZOIC ACID FORMUL 3 IOD I 1- FORMUL 4 DY6 2(C23 H20 N2 O5 S) FORMUL 6 HOH *31(H2 O) HELIX 1 1 VAL A 208 PHE A 226 1 19 HELIX 2 2 THR A 229 LEU A 237 1 9 HELIX 3 3 ASP A 251 LYS A 260 1 10 HELIX 4 4 GLU A 276 SER A 302 1 27 HELIX 5 5 ILE A 303 SER A 308 1 6 HELIX 6 6 PHE A 310 ALA A 331 1 22 HELIX 7 7 SER A 332 VAL A 334 5 3 HELIX 8 8 ALA A 342 GLY A 344 5 3 HELIX 9 9 ARG A 350 SER A 355 1 6 HELIX 10 10 PHE A 360 ALA A 376 1 17 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 TYR A 430 GLU A 460 1 31 HELIX 14 14 HIS A 466 LYS A 474 1 9 HELIX 15 15 ASP B 210 PHE B 226 1 17 HELIX 16 16 THR B 229 LEU B 237 1 9 HELIX 17 17 ASP B 251 LYS B 260 1 10 HELIX 18 18 GLU B 276 SER B 302 1 27 HELIX 19 19 ILE B 303 SER B 308 1 6 HELIX 20 20 PHE B 310 ALA B 331 1 22 HELIX 21 21 SER B 332 VAL B 334 5 3 HELIX 22 22 ARG B 350 SER B 355 1 6 HELIX 23 23 PHE B 360 ALA B 376 1 17 HELIX 24 24 ASP B 380 LEU B 393 1 14 HELIX 25 25 ASN B 402 HIS B 425 1 24 HELIX 26 26 TYR B 430 GLU B 460 1 31 HELIX 27 27 HIS B 466 LYS B 474 1 9 SHEET 1 A 3 PHE A 247 ILE A 249 0 SHEET 2 A 3 GLY A 346 THR A 349 1 O PHE A 347 N ILE A 249 SHEET 3 A 3 GLY A 338 VAL A 341 -1 N LEU A 339 O VAL A 348 SHEET 1 B 3 PHE B 247 ILE B 249 0 SHEET 2 B 3 GLY B 346 THR B 349 1 O PHE B 347 N ILE B 249 SHEET 3 B 3 GLY B 338 VAL B 341 -1 N LEU B 339 O VAL B 348 CISPEP 1 LYS A 358 PRO A 359 0 0.42 CISPEP 2 LYS B 358 PRO B 359 0 1.30 SITE 1 AC1 11 ARG A 284 CYS A 285 THR A 288 THR A 289 SITE 2 AC1 11 PHE A 327 LEU A 330 LEU A 339 ILE A 364 SITE 3 AC1 11 LYS A 367 HIS A 449 TYR A 473 SITE 1 AC2 10 TRP B 264 CYS B 285 THR B 288 THR B 289 SITE 2 AC2 10 PHE B 327 LEU B 330 LEU B 339 ILE B 364 SITE 3 AC2 10 HIS B 449 TYR B 473 CRYST1 39.886 94.324 97.066 90.00 98.30 90.00 P 1 21 1 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 0.025071 0.000000 0.003659 0.00000 SCALE2 0.000000 0.010602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010411 0.00000