HEADER TRANSCRIPTION 17-MAR-19 6JNO TITLE RXRA STRUCTURE COMPLEXED WITH CU-6PMN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: NUCLEAR RECEPTOR SUBFAMILY 2 GROUP B MEMBER 1,RETINOID X COMPND 5 RECEPTOR ALPHA; COMPND 6 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, LIGAND BINDING DOMAIN, FLUORESCENT KEYWDS 2 REAGENT, INACTIVE FORM, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.KAWASAKI,S.NAKANO,T.MOTOYAMA,S.YAMADA,M.WATANABE,Y.TAKAMURA, AUTHOR 2 M.FUJIHARA,H.TOKIWA,H.KAKUTA,S.ITO REVDAT 3 22-NOV-23 6JNO 1 REMARK REVDAT 2 04-DEC-19 6JNO 1 JRNL REVDAT 1 20-NOV-19 6JNO 0 SPRSDE 20-NOV-19 6JNO 5GYM JRNL AUTH S.YAMADA,M.KAWASAKI,M.FUJIHARA,M.WATANABE,Y.TAKAMURA, JRNL AUTH 2 M.TAKIOKU,H.NISHIOKA,Y.TAKEUCHI,M.MAKISHIMA,T.MOTOYAMA, JRNL AUTH 3 S.ITO,H.TOKIWA,S.NAKANO,H.KAKUTA JRNL TITL COMPETITIVE BINDING ASSAY WITH AN UMBELLIFERONE-BASED JRNL TITL 2 FLUORESCENT REXINOID FOR RETINOID X RECEPTOR LIGAND JRNL TITL 3 SCREENING. JRNL REF J.MED.CHEM. V. 62 8809 2019 JRNL REFN ISSN 0022-2623 JRNL PMID 31483660 JRNL DOI 10.1021/ACS.JMEDCHEM.9B00995 REMARK 2 REMARK 2 RESOLUTION. 2.65 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 27286 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1425 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) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1973 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.82 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 88 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6262 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 57 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.03000 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): 1.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.358 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.311 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.419 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.918 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.883 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6424 ; 0.003 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6281 ; 0.000 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8683 ; 1.132 ; 1.632 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14522 ; 1.083 ; 1.573 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 782 ; 7.490 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 318 ;31.906 ;21.447 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1163 ;19.783 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;23.392 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 823 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6995 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1334 ; 0.000 ; 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): 3155 ; 5.432 ; 5.087 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3154 ; 5.426 ; 5.086 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3928 ; 7.953 ; 7.621 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3929 ; 7.953 ; 7.623 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3269 ; 5.871 ; 5.603 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3270 ; 5.871 ; 5.604 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4756 ; 8.988 ; 8.211 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7171 ;12.032 ;60.438 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7172 ;12.031 ;60.435 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 264 458 B 264 458 6230 0.05 0.05 REMARK 3 2 A 264 454 C 264 454 6000 0.08 0.05 REMARK 3 3 A 264 454 D 264 454 6037 0.08 0.05 REMARK 3 4 B 264 454 C 264 454 5986 0.08 0.05 REMARK 3 5 B 264 454 D 264 454 6036 0.08 0.05 REMARK 3 6 C 231 455 D 231 455 6421 0.09 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6JNO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1300011436. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 1.00 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 : 27286 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 46.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.13400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.71600 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5GYM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) POLYETHYLENE GLYCOL 3350, REMARK 280 0.2M MG(OAC)2, PH 8.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 49.69300 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: 10340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 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 PRO B 231 REMARK 465 VAL B 232 REMARK 465 GLU B 233 REMARK 465 ARG B 234 REMARK 465 ILE B 235 REMARK 465 LEU B 236 REMARK 465 GLU B 237 REMARK 465 ALA B 238 REMARK 465 GLU B 239 REMARK 465 LEU B 240 REMARK 465 ALA B 241 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 ALA B 327 REMARK 465 THR B 328 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 VAL C 242 REMARK 465 GLU C 243 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 327 REMARK 465 THR C 328 REMARK 465 GLY C 329 REMARK 465 GLU C 456 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 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 ALA D 327 REMARK 465 THR D 328 REMARK 465 GLU D 456 REMARK 465 ALA D 457 REMARK 465 PRO D 458 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU C 239 NH1 ARG C 371 2.09 REMARK 500 NZ LYS A 417 OE2 GLU C 390 2.13 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 ND1 HIS B 338 ND2 ASN C 335 1455 2.07 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 PRO A 264 CA - N - CD ANGL. DEV. = -8.4 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 -11.36 85.74 REMARK 500 GLN A 411 70.32 -111.65 REMARK 500 ASP A 444 -72.23 -50.61 REMARK 500 HIS B 288 -12.78 87.56 REMARK 500 GLN B 411 70.84 -110.72 REMARK 500 ASP B 444 -76.57 -45.16 REMARK 500 ASN C 267 20.26 -65.59 REMARK 500 ILE C 268 -31.28 -37.25 REMARK 500 HIS C 288 -13.52 88.29 REMARK 500 GLN C 411 72.56 -111.84 REMARK 500 ASP C 444 -74.11 -49.75 REMARK 500 MET C 452 16.68 -67.49 REMARK 500 GLU C 453 32.29 -85.29 REMARK 500 ASP D 263 80.59 32.91 REMARK 500 HIS D 288 -13.98 88.16 REMARK 500 ASP D 322 47.16 37.20 REMARK 500 GLN D 411 72.11 -112.49 REMARK 500 ASP D 444 -75.20 -46.74 REMARK 500 MET D 452 14.56 -65.53 REMARK 500 GLU D 453 49.41 -80.05 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 ASN C 267 ILE C 268 134.27 REMARK 500 MET C 452 GLU C 453 148.31 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 WY5 A 501 DBREF 6JNO A 224 462 UNP P19793 RXRA_HUMAN 224 462 DBREF 6JNO B 224 462 UNP P19793 RXRA_HUMAN 224 462 DBREF 6JNO C 224 462 UNP P19793 RXRA_HUMAN 224 462 DBREF 6JNO D 224 462 UNP P19793 RXRA_HUMAN 224 462 SEQADV 6JNO GLY A 220 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER A 221 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER A 222 UNP P19793 EXPRESSION TAG SEQADV 6JNO HIS A 223 UNP P19793 EXPRESSION TAG SEQADV 6JNO GLY B 220 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER B 221 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER B 222 UNP P19793 EXPRESSION TAG SEQADV 6JNO HIS B 223 UNP P19793 EXPRESSION TAG SEQADV 6JNO GLY C 220 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER C 221 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER C 222 UNP P19793 EXPRESSION TAG SEQADV 6JNO HIS C 223 UNP P19793 EXPRESSION TAG SEQADV 6JNO GLY D 220 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER D 221 UNP P19793 EXPRESSION TAG SEQADV 6JNO SER D 222 UNP P19793 EXPRESSION TAG SEQADV 6JNO 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 WY5 A 501 30 HETNAM WY5 7-OXIDANYL-2-OXIDANYLIDENE-6-(3,5,5,8,8-PENTAMETHYL-6, HETNAM 2 WY5 7-DIHYDRONAPHTHALEN-2-YL)CHROMENE-3-CARBOXYLIC ACID FORMUL 5 WY5 C25 H26 O5 FORMUL 6 HOH *57(H2 O) HELIX 1 AA1 PRO A 264 ILE A 286 1 23 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 ALA A 457 1 22 HELIX 13 AB4 VAL B 265 ARG B 285 1 21 HELIX 14 AB5 HIS B 288 LEU B 292 5 5 HELIX 15 AB6 PRO B 293 SER B 317 1 25 HELIX 16 AB7 ILE B 318 VAL B 320 5 3 HELIX 17 AB8 ARG B 334 ALA B 340 1 7 HELIX 18 AB9 VAL B 342 LEU B 353 1 12 HELIX 19 AC1 LEU B 353 MET B 360 1 8 HELIX 20 AC2 ASP B 363 PHE B 376 1 14 HELIX 21 AC3 ASN B 385 TYR B 408 1 24 HELIX 22 AC4 GLY B 413 LEU B 420 1 8 HELIX 23 AC5 ARG B 421 LEU B 436 1 16 HELIX 24 AC6 LEU B 436 GLY B 443 1 8 HELIX 25 AC7 GLY B 443 ALA B 457 1 15 HELIX 26 AC8 VAL C 232 ALA C 241 1 10 HELIX 27 AC9 VAL C 265 ASN C 267 5 3 HELIX 28 AD1 ILE C 268 ILE C 286 1 19 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 ARG C 334 ALA C 340 1 7 HELIX 33 AD6 VAL C 342 LEU C 353 1 12 HELIX 34 AD7 LEU C 353 MET C 360 1 8 HELIX 35 AD8 ASP C 363 PHE C 376 1 14 HELIX 36 AD9 ASN C 385 TYR C 408 1 24 HELIX 37 AE1 GLY C 413 LEU C 420 1 8 HELIX 38 AE2 ARG C 421 LEU C 436 1 16 HELIX 39 AE3 LEU C 436 MET C 452 1 17 HELIX 40 AE4 VAL D 232 LEU D 240 1 9 HELIX 41 AE5 ASP D 263 ARG D 285 1 23 HELIX 42 AE6 HIS D 288 LEU D 292 5 5 HELIX 43 AE7 PRO D 293 SER D 317 1 25 HELIX 44 AE8 ILE D 318 VAL D 320 5 3 HELIX 45 AE9 ARG D 334 ALA D 340 1 7 HELIX 46 AF1 VAL D 342 LEU D 353 1 12 HELIX 47 AF2 LEU D 353 MET D 360 1 8 HELIX 48 AF3 ASP D 363 PHE D 376 1 14 HELIX 49 AF4 ASN D 385 TYR D 408 1 24 HELIX 50 AF5 GLY D 413 LEU D 420 1 8 HELIX 51 AF6 ARG D 421 HIS D 435 1 15 HELIX 52 AF7 LEU D 436 MET D 452 1 17 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 GLY B 323 LEU B 325 0 SHEET 2 AA2 2 HIS B 331 HIS B 333 -1 O VAL B 332 N ILE B 324 SHEET 1 AA3 2 GLY C 323 ILE C 324 0 SHEET 2 AA3 2 VAL C 332 HIS C 333 -1 O VAL C 332 N ILE C 324 SHEET 1 AA4 2 GLY D 323 LEU D 325 0 SHEET 2 AA4 2 HIS D 331 HIS D 333 -1 O VAL D 332 N ILE D 324 SSBOND 1 CYS A 269 CYS D 269 1555 1555 2.05 SSBOND 2 CYS B 269 CYS C 269 1555 1555 2.03 SITE 1 AC1 8 SER A 339 LEU A 436 PHE A 439 LYS A 440 SITE 2 AC1 8 ASP A 444 ARG D 302 TRP D 305 LEU D 433 CRYST1 46.615 99.386 110.158 90.00 99.42 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 0.021452 0.000000 0.003560 0.00000 SCALE2 0.000000 0.010062 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009202 0.00000