HEADER NUCLEAR PROTEIN 09-NOV-22 8HF8 TITLE HUMAN PPAR DELTA LIGAND BINDING DOMAIN IN COMPLEX WITH A SYNTHETIC TITLE 2 AGONIST V1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR DELTA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ACTIVATED RECEPTOR LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: PPAR-DELTA,NUCI,NUCLEAR HORMONE RECEPTOR 1,NUC1,NUCLEAR COMPND 6 RECEPTOR SUBFAMILY 1 GROUP C MEMBER 2,PEROXISOME PROLIFERATOR- COMPND 7 ACTIVATED RECEPTOR BETA,PPAR-BETA; COMPND 8 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: PPARD, NR1C2, PPARB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, AGONIST, PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR, NUCLEAR KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.DAI,H.B.SUN,H.L.YUAN,Z.Q.FENG REVDAT 1 06-SEP-23 8HF8 0 JRNL AUTH Z.FENG,J.XIANG,G.SUN,H.LIU,Y.WANG,X.LIU,J.FENG,Q.XU,X.WEN, JRNL AUTH 2 H.YUAN,H.SUN,L.DAI JRNL TITL DISCOVERY OF THE FIRST SUBNANOMOLAR PPAR ALPHA / DELTA DUAL JRNL TITL 2 AGONIST FOR THE TREATMENT OF CHOLESTATIC LIVER DISEASES. JRNL REF J.MED.CHEM. V. 66 7331 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 37243609 JRNL DOI 10.1021/ACS.JMEDCHEM.2C02123 REMARK 2 REMARK 2 RESOLUTION. 2.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 37883 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 1995 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 32.2600 - 5.0800 0.82 2288 128 0.1874 0.1701 REMARK 3 2 5.0800 - 4.0400 0.89 2419 135 0.1694 0.2148 REMARK 3 3 4.0400 - 3.5300 0.91 2509 140 0.1778 0.1807 REMARK 3 4 3.5300 - 3.2100 0.94 2563 142 0.2059 0.2464 REMARK 3 5 3.2100 - 2.9800 0.96 2613 146 0.2203 0.2808 REMARK 3 6 2.9800 - 2.8000 0.96 2603 145 0.2177 0.2555 REMARK 3 7 2.8000 - 2.6600 0.97 2629 145 0.2138 0.2676 REMARK 3 8 2.6600 - 2.5400 0.98 2694 151 0.2175 0.2754 REMARK 3 9 2.5400 - 2.4500 0.98 2649 145 0.2110 0.2493 REMARK 3 10 2.4500 - 2.3600 0.97 2599 145 0.2060 0.2537 REMARK 3 11 2.3600 - 2.2900 0.98 2696 149 0.2055 0.2462 REMARK 3 12 2.2900 - 2.2200 0.98 2642 147 0.2227 0.2805 REMARK 3 13 2.2200 - 2.1600 0.96 2620 146 0.2334 0.2843 REMARK 3 14 2.1600 - 2.1100 0.88 2364 131 0.2513 0.3082 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.53 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 8HF8 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_1300033217. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-22 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 : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37883 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.110 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 (%) : 95.0 REMARK 200 DATA REDUNDANCY : 2.700 REMARK 200 R MERGE (I) : 0.12300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12300 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: SIR REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M SODIUM CITRATE, PH 5.5, 19 % PEG REMARK 280 3350, 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K 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 46.48300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 MET A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 REMARK 465 LEU A 203 REMARK 465 VAL A 204 REMARK 465 PRO A 205 REMARK 465 ARG A 206 REMARK 465 GLY A 207 REMARK 465 SER A 208 REMARK 465 GLN A 266 REMARK 465 LEU A 267 REMARK 465 VAL A 268 REMARK 465 ASN A 269 REMARK 465 GLY A 270 REMARK 465 MET A 476 REMARK 465 TYR A 477 REMARK 465 MET B 196 REMARK 465 HIS B 197 REMARK 465 HIS B 198 REMARK 465 HIS B 199 REMARK 465 HIS B 200 REMARK 465 HIS B 201 REMARK 465 HIS B 202 REMARK 465 LEU B 203 REMARK 465 VAL B 204 REMARK 465 PRO B 205 REMARK 465 ARG B 206 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 LYS A 212 CG CD CE NZ REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 SER A 242 OG REMARK 470 HIS A 243 CG ND1 CD2 CE1 NE2 REMARK 470 THR A 244 OG1 CG2 REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 LYS A 336 CE NZ REMARK 470 SER B 208 OG REMARK 470 LYS B 212 CG CD CE NZ REMARK 470 LYS B 260 CD CE NZ REMARK 470 LEU B 262 CG CD1 CD2 REMARK 470 LYS B 336 CE NZ REMARK 470 GLU B 462 CG CD OE1 OE2 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 O ALA A 209 O HOH A 601 1.82 REMARK 500 OE2 GLU A 418 O HOH A 602 1.91 REMARK 500 O LEU B 400 O HOH B 601 1.92 REMARK 500 O HOH B 682 O HOH B 686 1.94 REMARK 500 O HOH A 611 O HOH A 669 1.99 REMARK 500 O HOH B 677 O HOH B 681 2.00 REMARK 500 O HOH A 717 O HOH A 722 2.07 REMARK 500 O HOH A 707 O HOH A 725 2.07 REMARK 500 NZ LYS A 224 O HOH A 603 2.09 REMARK 500 O HOH A 725 O HOH A 749 2.09 REMARK 500 O ILE B 303 O HOH B 602 2.09 REMARK 500 NH2 ARG A 455 O HOH A 604 2.12 REMARK 500 O HOH A 733 O HOH A 735 2.12 REMARK 500 O2 BOG B 502 O HOH B 603 2.12 REMARK 500 O SER B 208 O HOH B 604 2.13 REMARK 500 O HOH A 729 O HOH A 736 2.18 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 O HOH A 694 O HOH A 739 1655 1.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLN A 429 C TYR A 430 N -0.179 REMARK 500 TYR A 430 C LEU A 431 N -0.386 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 GLU A 378 OE1 - CD - OE2 ANGL. DEV. = 7.5 DEGREES REMARK 500 TYR A 430 O - C - N ANGL. DEV. = -10.8 DEGREES REMARK 500 LYS B 358 C - N - CA ANGL. DEV. = -18.0 DEGREES REMARK 500 PRO B 426 CB - CA - C ANGL. DEV. = 24.6 DEGREES REMARK 500 GLN B 444 C - N - CA ANGL. DEV. = -18.2 DEGREES REMARK 500 GLN B 444 CB - CG - CD ANGL. DEV. = -15.9 DEGREES REMARK 500 LEU B 465 CB - CG - CD1 ANGL. DEV. = 12.7 DEGREES REMARK 500 LYS B 474 CB - CA - C ANGL. DEV. = -18.5 DEGREES REMARK 500 LYS B 474 CA - CB - CG ANGL. DEV. = -14.5 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 THR A 244 -66.76 -121.17 REMARK 500 LYS A 260 33.85 -87.98 REMARK 500 ASN A 402 79.47 -108.11 REMARK 500 ASP A 427 46.05 -90.78 REMARK 500 TYR A 430 24.85 82.93 REMARK 500 GLU A 460 63.86 -104.23 REMARK 500 ALA B 209 -29.86 77.77 REMARK 500 THR B 238 -162.62 -127.81 REMARK 500 LYS B 260 36.18 -95.74 REMARK 500 ASN B 402 76.99 -110.06 REMARK 500 PRO B 426 -86.03 -6.23 REMARK 500 ASP B 427 -62.26 -103.35 REMARK 500 GLU B 460 63.58 -102.60 REMARK 500 LYS B 474 125.53 -39.48 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 LYS B 358 PRO B 359 90.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 429 10.17 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 B 691 DISTANCE = 7.17 ANGSTROMS DBREF 8HF8 A 209 477 UNP Q03181 PPARD_HUMAN 173 441 DBREF 8HF8 B 209 477 UNP Q03181 PPARD_HUMAN 173 441 SEQADV 8HF8 MET A 196 UNP Q03181 INITIATING METHIONINE SEQADV 8HF8 HIS A 197 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS A 198 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS A 199 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS A 200 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS A 201 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS A 202 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 LEU A 203 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 VAL A 204 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 PRO A 205 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 ARG A 206 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 GLY A 207 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 SER A 208 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 MET B 196 UNP Q03181 INITIATING METHIONINE SEQADV 8HF8 HIS B 197 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS B 198 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS B 199 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS B 200 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS B 201 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 HIS B 202 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 LEU B 203 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 VAL B 204 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 PRO B 205 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 ARG B 206 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 GLY B 207 UNP Q03181 EXPRESSION TAG SEQADV 8HF8 SER B 208 UNP Q03181 EXPRESSION TAG SEQRES 1 A 282 MET HIS HIS HIS HIS HIS HIS LEU VAL PRO ARG GLY SER SEQRES 2 A 282 ALA ASP LEU LYS ALA PHE SER LYS HIS ILE TYR ASN ALA SEQRES 3 A 282 TYR LEU LYS ASN PHE ASN MET THR LYS LYS LYS ALA ARG SEQRES 4 A 282 SER ILE LEU THR GLY LYS ALA SER HIS THR ALA PRO PHE SEQRES 5 A 282 VAL ILE HIS ASP ILE GLU THR LEU TRP GLN ALA GLU LYS SEQRES 6 A 282 GLY LEU VAL TRP LYS GLN LEU VAL ASN GLY LEU PRO PRO SEQRES 7 A 282 TYR LYS GLU ILE SER VAL HIS VAL PHE TYR ARG CYS GLN SEQRES 8 A 282 CYS THR THR VAL GLU THR VAL ARG GLU LEU THR GLU PHE SEQRES 9 A 282 ALA LYS SER ILE PRO SER PHE SER SER LEU PHE LEU ASN SEQRES 10 A 282 ASP GLN VAL THR LEU LEU LYS TYR GLY VAL HIS GLU ALA SEQRES 11 A 282 ILE PHE ALA MET LEU ALA SER ILE VAL ASN LYS ASP GLY SEQRES 12 A 282 LEU LEU VAL ALA ASN GLY SER GLY PHE VAL THR ARG GLU SEQRES 13 A 282 PHE LEU ARG SER LEU ARG LYS PRO PHE SER ASP ILE ILE SEQRES 14 A 282 GLU PRO LYS PHE GLU PHE ALA VAL LYS PHE ASN ALA LEU SEQRES 15 A 282 GLU LEU ASP ASP SER ASP LEU ALA LEU PHE ILE ALA ALA SEQRES 16 A 282 ILE ILE LEU CYS GLY ASP ARG PRO GLY LEU MET ASN VAL SEQRES 17 A 282 PRO ARG VAL GLU ALA ILE GLN ASP THR ILE LEU ARG ALA SEQRES 18 A 282 LEU GLU PHE HIS LEU GLN ALA ASN HIS PRO ASP ALA GLN SEQRES 19 A 282 TYR LEU PHE PRO LYS LEU LEU GLN LYS MET ALA ASP LEU SEQRES 20 A 282 ARG GLN LEU VAL THR GLU HIS ALA GLN MET MET GLN ARG SEQRES 21 A 282 ILE LYS LYS THR GLU THR GLU THR SER LEU HIS PRO LEU SEQRES 22 A 282 LEU GLN GLU ILE TYR LYS ASP MET TYR SEQRES 1 B 282 MET HIS HIS HIS HIS HIS HIS LEU VAL PRO ARG GLY SER SEQRES 2 B 282 ALA ASP LEU LYS ALA PHE SER LYS HIS ILE TYR ASN ALA SEQRES 3 B 282 TYR LEU LYS ASN PHE ASN MET THR LYS LYS LYS ALA ARG SEQRES 4 B 282 SER ILE LEU THR GLY LYS ALA SER HIS THR ALA PRO PHE SEQRES 5 B 282 VAL ILE HIS ASP ILE GLU THR LEU TRP GLN ALA GLU LYS SEQRES 6 B 282 GLY LEU VAL TRP LYS GLN LEU VAL ASN GLY LEU PRO PRO SEQRES 7 B 282 TYR LYS GLU ILE SER VAL HIS VAL PHE TYR ARG CYS GLN SEQRES 8 B 282 CYS THR THR VAL GLU THR VAL ARG GLU LEU THR GLU PHE SEQRES 9 B 282 ALA LYS SER ILE PRO SER PHE SER SER LEU PHE LEU ASN SEQRES 10 B 282 ASP GLN VAL THR LEU LEU LYS TYR GLY VAL HIS GLU ALA SEQRES 11 B 282 ILE PHE ALA MET LEU ALA SER ILE VAL ASN LYS ASP GLY SEQRES 12 B 282 LEU LEU VAL ALA ASN GLY SER GLY PHE VAL THR ARG GLU SEQRES 13 B 282 PHE LEU ARG SER LEU ARG LYS PRO PHE SER ASP ILE ILE SEQRES 14 B 282 GLU PRO LYS PHE GLU PHE ALA VAL LYS PHE ASN ALA LEU SEQRES 15 B 282 GLU LEU ASP ASP SER ASP LEU ALA LEU PHE ILE ALA ALA SEQRES 16 B 282 ILE ILE LEU CYS GLY ASP ARG PRO GLY LEU MET ASN VAL SEQRES 17 B 282 PRO ARG VAL GLU ALA ILE GLN ASP THR ILE LEU ARG ALA SEQRES 18 B 282 LEU GLU PHE HIS LEU GLN ALA ASN HIS PRO ASP ALA GLN SEQRES 19 B 282 TYR LEU PHE PRO LYS LEU LEU GLN LYS MET ALA ASP LEU SEQRES 20 B 282 ARG GLN LEU VAL THR GLU HIS ALA GLN MET MET GLN ARG SEQRES 21 B 282 ILE LYS LYS THR GLU THR GLU THR SER LEU HIS PRO LEU SEQRES 22 B 282 LEU GLN GLU ILE TYR LYS ASP MET TYR HET LOO A 501 33 HET BOG A 502 48 HET LOO B 501 33 HET BOG B 502 48 HETNAM LOO 2-[4-[[2,5-BIS(OXIDANYLIDENE)-3-[4-(TRIFLUOROMETHYL) HETNAM 2 LOO PHENYL]IMIDAZOLIDIN-1-YL]METHYL]-2,6-DIMETHYL- HETNAM 3 LOO PHENOXY]-2-METHYL-PROPANOIC ACID HETNAM BOG OCTYL BETA-D-GLUCOPYRANOSIDE HETSYN BOG BETA-OCTYLGLUCOSIDE; OCTYL BETA-D-GLUCOSIDE; OCTYL D- HETSYN 2 BOG GLUCOSIDE; OCTYL GLUCOSIDE FORMUL 3 LOO 2(C23 H23 F3 N2 O5) FORMUL 4 BOG 2(C14 H28 O6) FORMUL 7 HOH *240(H2 O) HELIX 1 AA1 ALA A 209 PHE A 226 1 18 HELIX 2 AA2 THR A 229 THR A 238 1 10 HELIX 3 AA3 ASP A 251 LYS A 260 1 10 HELIX 4 AA4 GLU A 276 SER A 302 1 27 HELIX 5 AA5 ILE A 303 LEU A 309 1 7 HELIX 6 AA6 PHE A 310 ALA A 331 1 22 HELIX 7 AA7 ARG A 350 SER A 355 1 6 HELIX 8 AA8 PRO A 359 ALA A 376 1 18 HELIX 9 AA9 ASP A 380 LEU A 393 1 14 HELIX 10 AB1 ASN A 402 HIS A 425 1 24 HELIX 11 AB2 TYR A 430 GLU A 460 1 31 HELIX 12 AB3 HIS A 466 LYS A 474 1 9 HELIX 13 AB4 ALA B 209 PHE B 226 1 18 HELIX 14 AB5 THR B 229 THR B 238 1 10 HELIX 15 AB6 ASP B 251 LYS B 260 1 10 HELIX 16 AB7 GLU B 276 SER B 302 1 27 HELIX 17 AB8 ILE B 303 LEU B 309 5 7 HELIX 18 AB9 PHE B 310 ALA B 331 1 22 HELIX 19 AC1 ARG B 350 SER B 355 1 6 HELIX 20 AC2 PRO B 359 ALA B 376 1 18 HELIX 21 AC3 ASP B 380 LEU B 393 1 14 HELIX 22 AC4 ASN B 402 ALA B 423 1 22 HELIX 23 AC5 TYR B 430 GLU B 460 1 31 HELIX 24 AC6 HIS B 466 LYS B 474 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 VAL A 341 -1 N LEU A 339 O VAL A 348 SHEET 4 AA1 4 VAL A 334 ASN A 335 -1 N ASN A 335 O GLY A 338 SHEET 1 AA2 4 PHE B 247 ILE B 249 0 SHEET 2 AA2 4 GLY B 346 THR B 349 1 O PHE B 347 N ILE B 249 SHEET 3 AA2 4 GLY B 338 VAL B 341 -1 N LEU B 339 O VAL B 348 SHEET 4 AA2 4 VAL B 334 ASN B 335 -1 N ASN B 335 O GLY B 338 CISPEP 1 LYS A 358 PRO A 359 0 4.41 CRYST1 39.795 92.966 96.715 90.00 96.00 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 0.025129 0.000000 0.002641 0.00000 SCALE2 0.000000 0.010757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010397 0.00000