HEADER NUCLEAR PROTEIN 27-JUN-20 7CFO TITLE CRYSTAL STRUCTURE OF HUMAN RXRALPHA LIGAND BINDING DOMAIN COMPLEXED TITLE 2 WITH CBTF-EE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 6 RECEPTOR ALPHA; COMPND 7 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: RXRA, NR2B1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RETINOID X RECEPTOR ALPHA, ANTAGONIST, NUCLEAR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.WATANABE,M.FUJIHARA,T.MOTOYAMA,M.KAWASAKI,S.YAMADA,Y.TAKAMURA, AUTHOR 2 S.ITO,M.MAKISHIMA,S.NAKANO,H.KAKUTA REVDAT 4 29-NOV-23 7CFO 1 REMARK REVDAT 3 27-JAN-21 7CFO 1 JRNL REVDAT 2 13-JAN-21 7CFO 1 JRNL REVDAT 1 06-JAN-21 7CFO 0 JRNL AUTH M.WATANABE,M.FUJIHARA,T.MOTOYAMA,M.KAWASAKI,S.YAMADA, JRNL AUTH 2 Y.TAKAMURA,S.ITO,M.MAKISHIMA,S.NAKANO,H.KAKUTA JRNL TITL DISCOVERY OF A "GATEKEEPER" ANTAGONIST THAT BLOCKS ENTRY JRNL TITL 2 PATHWAY TO RETINOID X RECEPTORS (RXRS) WITHOUT ALLOSTERIC JRNL TITL 3 LIGAND INHIBITION IN PERMISSIVE RXR HETERODIMERS. JRNL REF J.MED.CHEM. V. 64 430 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33356247 JRNL DOI 10.1021/ACS.JMEDCHEM.0C01354 REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 45567 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) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2423 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2570 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2960 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6268 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.90 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) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.281 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.223 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.209 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.504 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6525 ; 0.009 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6362 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8834 ; 2.001 ; 1.661 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14704 ; 1.314 ; 1.592 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 784 ; 6.375 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 318 ;28.767 ;21.447 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1164 ;17.983 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;22.007 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 834 ; 0.232 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7047 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1346 ; 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): 3163 ; 4.743 ; 5.075 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3159 ; 4.731 ; 5.072 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3936 ; 6.564 ; 7.581 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3937 ; 6.564 ; 7.581 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3362 ; 5.421 ; 5.710 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3363 ; 5.420 ; 5.710 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4899 ; 7.997 ; 8.379 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7288 ;10.373 ;60.657 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7285 ;10.374 ;60.656 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 38 231 B 38 231 5970 0.11 0.05 REMARK 3 2 A 38 229 C 38 229 5827 0.10 0.05 REMARK 3 3 A 42 231 D 42 231 5798 0.08 0.05 REMARK 3 4 B 5 230 C 5 230 6264 0.11 0.05 REMARK 3 5 B 42 231 D 42 231 5699 0.11 0.05 REMARK 3 6 C 42 229 D 42 229 5617 0.11 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7CFO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1300017527. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48015 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 47.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 5ZQU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% [V/V] TACSIMATETM [PH 7.0], 0.1 M REMARK 280 HEPES [PH 7.0], AND 10% [W/V] PEGMME5000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K 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 49.71600 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 220 REMARK 465 SER A 221 REMARK 465 SER A 222 REMARK 465 HIS A 223 REMARK 465 SER A 224 REMARK 465 SER A 225 REMARK 465 ALA A 226 REMARK 465 ASN A 227 REMARK 465 GLU A 228 REMARK 465 ASP A 229 REMARK 465 MET A 230 REMARK 465 PRO A 231 REMARK 465 VAL A 232 REMARK 465 GLU A 233 REMARK 465 ARG A 234 REMARK 465 ILE A 235 REMARK 465 LEU A 236 REMARK 465 GLU A 237 REMARK 465 ALA A 238 REMARK 465 GLU A 239 REMARK 465 LEU A 240 REMARK 465 ALA A 241 REMARK 465 VAL A 242 REMARK 465 GLU A 243 REMARK 465 PRO A 244 REMARK 465 LYS A 245 REMARK 465 THR A 246 REMARK 465 GLU A 247 REMARK 465 THR A 248 REMARK 465 TYR A 249 REMARK 465 VAL A 250 REMARK 465 GLU A 251 REMARK 465 ALA A 252 REMARK 465 ASN A 253 REMARK 465 MET A 254 REMARK 465 GLY A 255 REMARK 465 LEU A 256 REMARK 465 ASN A 257 REMARK 465 PRO A 258 REMARK 465 SER A 259 REMARK 465 SER A 260 REMARK 465 PRO A 261 REMARK 465 ASN A 262 REMARK 465 ASP A 263 REMARK 465 THR A 328 REMARK 465 GLY A 329 REMARK 465 HIS A 459 REMARK 465 GLN A 460 REMARK 465 MET A 461 REMARK 465 THR A 462 REMARK 465 GLY B 220 REMARK 465 SER B 221 REMARK 465 SER B 222 REMARK 465 HIS B 223 REMARK 465 SER B 224 REMARK 465 SER B 225 REMARK 465 ALA B 226 REMARK 465 ASN B 227 REMARK 465 GLU B 228 REMARK 465 ASP B 229 REMARK 465 MET B 230 REMARK 465 VAL B 242 REMARK 465 GLU B 243 REMARK 465 PRO B 244 REMARK 465 LYS B 245 REMARK 465 THR B 246 REMARK 465 GLU B 247 REMARK 465 THR B 248 REMARK 465 TYR B 249 REMARK 465 VAL B 250 REMARK 465 GLU B 251 REMARK 465 ALA B 252 REMARK 465 ASN B 253 REMARK 465 MET B 254 REMARK 465 GLY B 255 REMARK 465 LEU B 256 REMARK 465 ASN B 257 REMARK 465 PRO B 258 REMARK 465 SER B 259 REMARK 465 SER B 260 REMARK 465 PRO B 261 REMARK 465 ASN B 262 REMARK 465 ASP B 263 REMARK 465 HIS B 459 REMARK 465 GLN B 460 REMARK 465 MET B 461 REMARK 465 THR B 462 REMARK 465 GLY C 220 REMARK 465 SER C 221 REMARK 465 SER C 222 REMARK 465 HIS C 223 REMARK 465 SER C 224 REMARK 465 SER C 225 REMARK 465 ALA C 226 REMARK 465 ASN C 227 REMARK 465 GLU C 228 REMARK 465 ASP C 229 REMARK 465 MET C 230 REMARK 465 PRO C 244 REMARK 465 LYS C 245 REMARK 465 THR C 246 REMARK 465 GLU C 247 REMARK 465 THR C 248 REMARK 465 TYR C 249 REMARK 465 VAL C 250 REMARK 465 GLU C 251 REMARK 465 ALA C 252 REMARK 465 ASN C 253 REMARK 465 MET C 254 REMARK 465 GLY C 255 REMARK 465 LEU C 256 REMARK 465 ASN C 257 REMARK 465 PRO C 258 REMARK 465 SER C 259 REMARK 465 SER C 260 REMARK 465 PRO C 261 REMARK 465 ASN C 262 REMARK 465 ASP C 263 REMARK 465 ALA C 457 REMARK 465 PRO C 458 REMARK 465 HIS C 459 REMARK 465 GLN C 460 REMARK 465 MET C 461 REMARK 465 THR C 462 REMARK 465 GLY D 220 REMARK 465 SER D 221 REMARK 465 SER D 222 REMARK 465 HIS D 223 REMARK 465 SER D 224 REMARK 465 SER D 225 REMARK 465 ALA D 226 REMARK 465 ASN D 227 REMARK 465 GLU D 228 REMARK 465 ASP D 229 REMARK 465 MET D 230 REMARK 465 PRO D 231 REMARK 465 VAL D 232 REMARK 465 GLU D 233 REMARK 465 ARG D 234 REMARK 465 ILE D 235 REMARK 465 LEU D 236 REMARK 465 GLU D 237 REMARK 465 ALA D 238 REMARK 465 GLU D 239 REMARK 465 LEU D 240 REMARK 465 ALA D 241 REMARK 465 VAL D 242 REMARK 465 GLU D 243 REMARK 465 PRO D 244 REMARK 465 LYS D 245 REMARK 465 THR D 246 REMARK 465 GLU D 247 REMARK 465 THR D 248 REMARK 465 TYR D 249 REMARK 465 VAL D 250 REMARK 465 GLU D 251 REMARK 465 ALA D 252 REMARK 465 ASN D 253 REMARK 465 MET D 254 REMARK 465 GLY D 255 REMARK 465 LEU D 256 REMARK 465 ASN D 257 REMARK 465 PRO D 258 REMARK 465 SER D 259 REMARK 465 SER D 260 REMARK 465 PRO D 261 REMARK 465 ASN D 262 REMARK 465 ASP D 263 REMARK 465 PRO D 264 REMARK 465 VAL D 265 REMARK 465 THR D 266 REMARK 465 ASN D 267 REMARK 465 ALA D 327 REMARK 465 THR D 328 REMARK 465 GLY D 329 REMARK 465 LEU D 330 REMARK 465 HIS D 459 REMARK 465 GLN D 460 REMARK 465 MET D 461 REMARK 465 THR D 462 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 ARG A 348 CB - CG - CD ANGL. DEV. = 16.9 DEGREES REMARK 500 ARG A 348 CG - CD - NE ANGL. DEV. = 12.9 DEGREES REMARK 500 PRO B 231 CA - N - CD ANGL. DEV. = -12.6 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 HIS A 288 -9.51 86.05 REMARK 500 GLN A 411 79.40 -117.52 REMARK 500 HIS B 288 -9.67 86.31 REMARK 500 LYS B 321 76.93 -117.24 REMARK 500 ASP B 322 -60.79 -175.05 REMARK 500 LEU B 326 49.13 -101.76 REMARK 500 ALA B 327 -56.17 89.00 REMARK 500 GLN B 411 76.60 -118.89 REMARK 500 HIS C 288 -8.04 85.37 REMARK 500 ARG C 334 35.66 157.99 REMARK 500 ASN C 335 -81.28 -116.58 REMARK 500 GLN C 411 76.38 -118.50 REMARK 500 HIS D 288 -8.46 86.50 REMARK 500 GLN D 411 77.64 -116.80 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 PRO B 231 VAL B 232 -145.15 REMARK 500 PRO B 264 VAL B 265 147.57 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 WZ6 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue WZ6 B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue WZ6 C 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 501 DBREF 7CFO A 224 462 UNP P19793 RXRA_HUMAN 224 462 DBREF 7CFO B 224 462 UNP P19793 RXRA_HUMAN 224 462 DBREF 7CFO C 224 462 UNP P19793 RXRA_HUMAN 224 462 DBREF 7CFO D 224 462 UNP P19793 RXRA_HUMAN 224 462 SEQADV 7CFO GLY A 220 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER A 221 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER A 222 UNP P19793 EXPRESSION TAG SEQADV 7CFO HIS A 223 UNP P19793 EXPRESSION TAG SEQADV 7CFO GLY B 220 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER B 221 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER B 222 UNP P19793 EXPRESSION TAG SEQADV 7CFO HIS B 223 UNP P19793 EXPRESSION TAG SEQADV 7CFO GLY C 220 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER C 221 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER C 222 UNP P19793 EXPRESSION TAG SEQADV 7CFO HIS C 223 UNP P19793 EXPRESSION TAG SEQADV 7CFO GLY D 220 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER D 221 UNP P19793 EXPRESSION TAG SEQADV 7CFO SER D 222 UNP P19793 EXPRESSION TAG SEQADV 7CFO HIS D 223 UNP P19793 EXPRESSION TAG SEQRES 1 A 243 GLY SER SER HIS SER SER ALA ASN GLU ASP MET PRO VAL SEQRES 2 A 243 GLU ARG ILE LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS SEQRES 3 A 243 THR GLU THR TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SEQRES 4 A 243 SER SER PRO ASN ASP PRO VAL THR ASN ILE CYS GLN ALA SEQRES 5 A 243 ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA LYS SEQRES 6 A 243 ARG ILE PRO HIS PHE SER GLU LEU PRO LEU ASP ASP GLN SEQRES 7 A 243 VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE SEQRES 8 A 243 ALA SER PHE SER HIS ARG SER ILE ALA VAL LYS ASP GLY SEQRES 9 A 243 ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG ASN SER SEQRES 10 A 243 ALA HIS SER ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL SEQRES 11 A 243 LEU THR GLU LEU VAL SER LYS MET ARG ASP MET GLN MET SEQRES 12 A 243 ASP LYS THR GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU SEQRES 13 A 243 PHE ASN PRO ASP SER LYS GLY LEU SER ASN PRO ALA GLU SEQRES 14 A 243 VAL GLU ALA LEU ARG GLU LYS VAL TYR ALA SER LEU GLU SEQRES 15 A 243 ALA TYR CYS LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG SEQRES 16 A 243 PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SER SEQRES 17 A 243 ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS SEQRES 18 A 243 LEU ILE GLY ASP THR PRO ILE ASP THR PHE LEU MET GLU SEQRES 19 A 243 MET LEU GLU ALA PRO HIS GLN MET THR SEQRES 1 B 243 GLY SER SER HIS SER SER ALA ASN GLU ASP MET PRO VAL SEQRES 2 B 243 GLU ARG ILE LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS SEQRES 3 B 243 THR GLU THR TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SEQRES 4 B 243 SER SER PRO ASN ASP PRO VAL THR ASN ILE CYS GLN ALA SEQRES 5 B 243 ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA LYS SEQRES 6 B 243 ARG ILE PRO HIS PHE SER GLU LEU PRO LEU ASP ASP GLN SEQRES 7 B 243 VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE SEQRES 8 B 243 ALA SER PHE SER HIS ARG SER ILE ALA VAL LYS ASP GLY SEQRES 9 B 243 ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG ASN SER SEQRES 10 B 243 ALA HIS SER ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL SEQRES 11 B 243 LEU THR GLU LEU VAL SER LYS MET ARG ASP MET GLN MET SEQRES 12 B 243 ASP LYS THR GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU SEQRES 13 B 243 PHE ASN PRO ASP SER LYS GLY LEU SER ASN PRO ALA GLU SEQRES 14 B 243 VAL GLU ALA LEU ARG GLU LYS VAL TYR ALA SER LEU GLU SEQRES 15 B 243 ALA TYR CYS LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG SEQRES 16 B 243 PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SER SEQRES 17 B 243 ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS SEQRES 18 B 243 LEU ILE GLY ASP THR PRO ILE ASP THR PHE LEU MET GLU SEQRES 19 B 243 MET LEU GLU ALA PRO HIS GLN MET THR SEQRES 1 C 243 GLY SER SER HIS SER SER ALA ASN GLU ASP MET PRO VAL SEQRES 2 C 243 GLU ARG ILE LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS SEQRES 3 C 243 THR GLU THR TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SEQRES 4 C 243 SER SER PRO ASN ASP PRO VAL THR ASN ILE CYS GLN ALA SEQRES 5 C 243 ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA LYS SEQRES 6 C 243 ARG ILE PRO HIS PHE SER GLU LEU PRO LEU ASP ASP GLN SEQRES 7 C 243 VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE SEQRES 8 C 243 ALA SER PHE SER HIS ARG SER ILE ALA VAL LYS ASP GLY SEQRES 9 C 243 ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG ASN SER SEQRES 10 C 243 ALA HIS SER ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL SEQRES 11 C 243 LEU THR GLU LEU VAL SER LYS MET ARG ASP MET GLN MET SEQRES 12 C 243 ASP LYS THR GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU SEQRES 13 C 243 PHE ASN PRO ASP SER LYS GLY LEU SER ASN PRO ALA GLU SEQRES 14 C 243 VAL GLU ALA LEU ARG GLU LYS VAL TYR ALA SER LEU GLU SEQRES 15 C 243 ALA TYR CYS LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG SEQRES 16 C 243 PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SER SEQRES 17 C 243 ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS SEQRES 18 C 243 LEU ILE GLY ASP THR PRO ILE ASP THR PHE LEU MET GLU SEQRES 19 C 243 MET LEU GLU ALA PRO HIS GLN MET THR SEQRES 1 D 243 GLY SER SER HIS SER SER ALA ASN GLU ASP MET PRO VAL SEQRES 2 D 243 GLU ARG ILE LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS SEQRES 3 D 243 THR GLU THR TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SEQRES 4 D 243 SER SER PRO ASN ASP PRO VAL THR ASN ILE CYS GLN ALA SEQRES 5 D 243 ALA ASP LYS GLN LEU PHE THR LEU VAL GLU TRP ALA LYS SEQRES 6 D 243 ARG ILE PRO HIS PHE SER GLU LEU PRO LEU ASP ASP GLN SEQRES 7 D 243 VAL ILE LEU LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE SEQRES 8 D 243 ALA SER PHE SER HIS ARG SER ILE ALA VAL LYS ASP GLY SEQRES 9 D 243 ILE LEU LEU ALA THR GLY LEU HIS VAL HIS ARG ASN SER SEQRES 10 D 243 ALA HIS SER ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL SEQRES 11 D 243 LEU THR GLU LEU VAL SER LYS MET ARG ASP MET GLN MET SEQRES 12 D 243 ASP LYS THR GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU SEQRES 13 D 243 PHE ASN PRO ASP SER LYS GLY LEU SER ASN PRO ALA GLU SEQRES 14 D 243 VAL GLU ALA LEU ARG GLU LYS VAL TYR ALA SER LEU GLU SEQRES 15 D 243 ALA TYR CYS LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG SEQRES 16 D 243 PHE ALA LYS LEU LEU LEU ARG LEU PRO ALA LEU ARG SER SEQRES 17 D 243 ILE GLY LEU LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS SEQRES 18 D 243 LEU ILE GLY ASP THR PRO ILE ASP THR PHE LEU MET GLU SEQRES 19 D 243 MET LEU GLU ALA PRO HIS GLN MET THR HET WZ6 A 500 36 HET WZ6 B 500 36 HET GOL B 501 6 HET WZ6 C 500 36 HET GOL C 501 6 HETNAM WZ6 1-[3-(2-ETHOXYETHOXY)-5,5,8,8-TETRAMETHYL-6,7- HETNAM 2 WZ6 DIHYDRONAPHTHALEN-2-YL]-2-(TRIFLUOROMETHYL) HETNAM 3 WZ6 BENZIMIDAZOLE-5-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 WZ6 3(C27 H31 F3 N2 O4) FORMUL 7 GOL 2(C3 H8 O3) FORMUL 10 HOH *93(H2 O) HELIX 1 AA1 VAL A 265 ARG A 285 1 21 HELIX 2 AA2 HIS A 288 LEU A 292 5 5 HELIX 3 AA3 PRO A 293 SER A 317 1 25 HELIX 4 AA4 ILE A 318 VAL A 320 5 3 HELIX 5 AA5 ARG A 334 ALA A 340 1 7 HELIX 6 AA6 VAL A 342 LEU A 353 1 12 HELIX 7 AA7 LEU A 353 MET A 360 1 8 HELIX 8 AA8 ASP A 363 PHE A 376 1 14 HELIX 9 AA9 ASN A 385 TYR A 408 1 24 HELIX 10 AB1 GLY A 413 LEU A 420 1 8 HELIX 11 AB2 ARG A 421 HIS A 435 1 15 HELIX 12 AB3 LEU A 436 ILE A 442 1 7 HELIX 13 AB4 GLY A 443 GLU A 456 1 14 HELIX 14 AB5 VAL B 232 ALA B 241 1 10 HELIX 15 AB6 VAL B 265 ARG B 285 1 21 HELIX 16 AB7 HIS B 288 LEU B 292 5 5 HELIX 17 AB8 PRO B 293 SER B 317 1 25 HELIX 18 AB9 ILE B 318 VAL B 320 5 3 HELIX 19 AC1 HIS B 333 ALA B 340 1 8 HELIX 20 AC2 VAL B 342 LEU B 353 1 12 HELIX 21 AC3 LEU B 353 MET B 360 1 8 HELIX 22 AC4 ASP B 363 PHE B 376 1 14 HELIX 23 AC5 ASN B 385 TYR B 408 1 24 HELIX 24 AC6 GLY B 413 LEU B 420 1 8 HELIX 25 AC7 ARG B 421 HIS B 435 1 15 HELIX 26 AC8 LEU B 436 ALA B 457 1 22 HELIX 27 AC9 VAL C 232 ALA C 241 1 10 HELIX 28 AD1 VAL C 265 ARG C 285 1 21 HELIX 29 AD2 HIS C 288 LEU C 292 5 5 HELIX 30 AD3 PRO C 293 SER C 317 1 25 HELIX 31 AD4 ILE C 318 VAL C 320 5 3 HELIX 32 AD5 ALA C 327 GLY C 329 5 3 HELIX 33 AD6 ASN C 335 GLY C 341 1 7 HELIX 34 AD7 VAL C 342 LEU C 353 1 12 HELIX 35 AD8 LEU C 353 MET C 360 1 8 HELIX 36 AD9 ASP C 363 PHE C 376 1 14 HELIX 37 AE1 ASN C 385 TYR C 408 1 24 HELIX 38 AE2 GLY C 413 LEU C 420 1 8 HELIX 39 AE3 ARG C 421 HIS C 435 1 15 HELIX 40 AE4 LEU C 436 GLY C 443 1 8 HELIX 41 AE5 GLY C 443 GLU C 456 1 14 HELIX 42 AE6 CYS D 269 ARG D 285 1 17 HELIX 43 AE7 HIS D 288 LEU D 292 5 5 HELIX 44 AE8 PRO D 293 SER D 317 1 25 HELIX 45 AE9 ILE D 318 VAL D 320 5 3 HELIX 46 AF1 ARG D 334 ALA D 340 1 7 HELIX 47 AF2 VAL D 342 LEU D 353 1 12 HELIX 48 AF3 LEU D 353 MET D 360 1 8 HELIX 49 AF4 ASP D 363 PHE D 376 1 14 HELIX 50 AF5 ASN D 385 TYR D 408 1 24 HELIX 51 AF6 GLY D 413 LEU D 420 1 8 HELIX 52 AF7 ARG D 421 HIS D 435 1 15 HELIX 53 AF8 LEU D 436 GLY D 443 1 8 HELIX 54 AF9 GLY D 443 GLU D 456 1 14 SHEET 1 AA1 2 GLY A 323 LEU A 325 0 SHEET 2 AA1 2 HIS A 331 HIS A 333 -1 O VAL A 332 N ILE A 324 SHEET 1 AA2 2 ILE B 324 LEU B 325 0 SHEET 2 AA2 2 HIS B 331 VAL B 332 -1 O VAL B 332 N ILE B 324 SHEET 1 AA3 2 ILE C 324 LEU C 325 0 SHEET 2 AA3 2 HIS C 331 VAL C 332 -1 O VAL C 332 N ILE C 324 SHEET 1 AA4 2 GLY D 323 ILE D 324 0 SHEET 2 AA4 2 VAL D 332 HIS D 333 -1 O VAL D 332 N ILE D 324 SSBOND 1 CYS A 269 CYS C 269 1555 1555 2.03 SSBOND 2 CYS B 269 CYS D 269 1555 1555 2.02 SITE 1 AC1 8 ILE A 268 TRP A 305 LEU A 436 PHE A 438 SITE 2 AC1 8 PHE A 439 PHE C 439 LYS C 440 WZ6 C 500 SITE 1 AC2 7 ALA B 272 TRP B 305 LEU B 433 PHE B 439 SITE 2 AC2 7 LEU D 436 PHE D 439 PHE D 450 SITE 1 AC3 4 GLU A 352 ASN B 377 ASP B 379 ARG B 426 SITE 1 AC4 10 LEU A 436 PHE A 439 ILE A 447 WZ6 A 500 SITE 2 AC4 10 ALA C 272 LEU C 433 PHE C 438 PHE C 439 SITE 3 AC4 10 ILE C 442 HOH C 611 SITE 1 AC5 3 ALA C 303 ARG C 426 SER D 427 CRYST1 50.757 99.432 93.598 90.00 98.31 90.00 P 1 21 1 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 0.019702 0.000000 0.002877 0.00000 SCALE2 0.000000 0.010057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010797 0.00000