PDB Short entry for 2ZY0 HEADER TRANSCRIPTION 09-JAN-09 2ZY0 TITLE CRYSTAL STRUCTURE OF THE HUMAN RXR ALPHA LIGAND BINDING DOMAIN BOUND TITLE 2 TO A SYNTHETIC AGONIST COMPOUND AND A COACTIVATOR PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RXR-ALPHA; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: RETINOID X RECEPTOR ALPHA, NUCLEAR RECEPTOR SUBFAMILY 2 COMPND 6 GROUP B MEMBER 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: GRIP1 FROM NUCLEAR RECEPTOR COACTIVATOR 2; COMPND 10 CHAIN: B, D; COMPND 11 SYNONYM: NCOA-2, TRANSCRIPTIONAL INTERMEDIARY FACTOR 2, HTIF2; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS. KEYWDS TRANSCRIPTION REGULATION, NUCLEAR RECEPTOR, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM FOR RESEARCH ON GENE EXPRESSION, KEYWDS 3 SGCGES, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.SATO,P.ANTONY,N.ROCHEL,D.MORAS,STRUCTURAL GENOMICS CONSORTIUM FOR AUTHOR 2 RESEARCH ON GENE EXPRESSION (SGCGES) REVDAT 2 11-OCT-17 2ZY0 1 REMARK REVDAT 1 11-AUG-09 2ZY0 0 JRNL AUTH W.P.LIPPERT,C.BURSCHKA,K.GOTZ,M.KAUPP,D.IVANOVA,C.GAUDON, JRNL AUTH 2 Y.SATO,P.ANTONY,N.ROCHEL,D.MORAS,H.GRONEMEYER,R.TACKE JRNL TITL SILICON ANALOGUES OF THE RXR-SELECTIVE RETINOID AGONIST JRNL TITL 2 SR11237 (BMS649): CHEMISTRY AND BIOLOGY JRNL REF CHEMMEDCHEM V. 4 1143 2009 JRNL REFN ISSN 1860-7179 JRNL PMID 19496083 JRNL DOI 10.1002/CMDC.200900090 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10834 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 512 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) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 662 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.14 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3581 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 26 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 65.99 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.37000 REMARK 3 B22 (A**2) : -1.60000 REMARK 3 B33 (A**2) : -3.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.508 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.380 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.332 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.927 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3716 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5041 ; 1.043 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 451 ; 4.309 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 160 ;38.676 ;23.625 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 664 ;15.385 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;23.301 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 574 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2746 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1697 ; 0.178 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2540 ; 0.293 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 84 ; 0.128 ; 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): 33 ; 0.166 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.049 ; 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): 2264 ; 0.268 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3644 ; 0.502 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1532 ; 0.552 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1394 ; 0.880 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 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: NULL REMARK 4 REMARK 4 2ZY0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000028567. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-SEP-07 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 : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND(111),GE(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11166 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 36.7670 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) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.31700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1MZN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM TRIS-HCL, 250MM NACL, 5MM DTT, REMARK 280 50MM CALCIUM ACETATE, 18% PEG3350, PH 8.0, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 32.48750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.39650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 55.39650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.48750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.42500 REMARK 290 SMTRY3 4 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 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 THR A 223 REMARK 465 SER A 224 REMARK 465 SER A 225 REMARK 465 ALA A 226 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 HIS A 459 REMARK 465 GLN A 460 REMARK 465 MET A 461 REMARK 465 THR A 462 REMARK 465 LYS B 471 REMARK 465 SER B 482 REMARK 465 SER B 483 REMARK 465 THR C 223 REMARK 465 SER C 224 REMARK 465 SER C 225 REMARK 465 ALA C 226 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 HIS C 459 REMARK 465 GLN C 460 REMARK 465 MET C 461 REMARK 465 THR C 462 REMARK 465 SER D 482 REMARK 465 SER D 483 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU A 228 CG CD OE1 OE2 REMARK 480 ASP A 229 CG OD1 OD2 REMARK 480 GLU A 243 OE1 OE2 REMARK 480 LEU A 330 CD1 CD2 REMARK 480 LYS A 381 CD CE NZ REMARK 480 GLU C 281 OE1 OE2 REMARK 480 ASP C 295 OD1 OD2 REMARK 480 LEU C 325 CD1 CD2 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 GLU A 243 CD GLU A 243 OE1 -0.172 REMARK 500 GLU A 243 CD GLU A 243 OE2 0.091 REMARK 500 LEU A 330 CG LEU A 330 CD1 -0.265 REMARK 500 GLU C 281 CD GLU C 281 OE1 0.445 REMARK 500 GLU C 281 CD GLU C 281 OE2 -0.190 REMARK 500 LEU C 325 CG LEU C 325 CD2 -0.240 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 LEU A 330 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES REMARK 500 GLU C 281 OE1 - CD - OE2 ANGL. DEV. = -20.2 DEGREES REMARK 500 GLU C 281 CG - CD - OE2 ANGL. DEV. = 18.4 DEGREES REMARK 500 ASP C 295 CB - CG - OD2 ANGL. DEV. = -14.7 DEGREES REMARK 500 LEU C 325 CB - CG - CD2 ANGL. DEV. = 13.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 322 54.93 -145.47 REMARK 500 GLU C 228 -82.18 -87.08 REMARK 500 HIS C 288 -4.96 75.59 REMARK 500 LEU C 353 -72.44 -108.04 REMARK 500 HIS D 472 81.15 42.81 REMARK 500 GLN D 480 -75.39 -77.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU C 281 0.09 SIDE CHAIN REMARK 500 ASP C 295 0.16 SIDE CHAIN 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 21P A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 21P C 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FBY RELATED DB: PDB REMARK 900 1FBY CONTAINS THE HUMAN RXR ALPHA LIGAND BINDING DOMAIN BOUND TO 9- REMARK 900 CIS RETINOIC ACID REMARK 900 RELATED ID: 1MVC RELATED DB: PDB REMARK 900 1MVC CONTAINS THE SAME PROTEIN COMPLEXED WITH BMS 649 REMARK 900 RELATED ID: 1MV9 RELATED DB: PDB REMARK 900 1MV9 CONTAINS THE SAME PROTEIN COMPLEXED WITH DHA (DOCOSA HEXAENOIC REMARK 900 ACID) REMARK 900 RELATED ID: 2ZXZ RELATED DB: PDB REMARK 900 2ZXZ CONTAINS THE SAME PROTEIN COMPLEXED WITH 4-[2-(1,1,3,3- REMARK 900 TETRAMETHYLINDAN-5-YL)-1,3-DIOXOLAN-2-YL]BENZOIC ACID DBREF 2ZY0 A 223 462 UNP P19793 RXRA_HUMAN 223 462 DBREF 2ZY0 B 471 483 UNP Q15596 NCOA2_HUMAN 686 698 DBREF 2ZY0 C 223 462 UNP P19793 RXRA_HUMAN 223 462 DBREF 2ZY0 D 471 483 UNP Q15596 NCOA2_HUMAN 686 698 SEQRES 1 A 240 THR SER SER ALA ASN GLU ASP MET PRO VAL GLU ARG ILE SEQRES 2 A 240 LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS THR GLU THR SEQRES 3 A 240 TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SER SER PRO SEQRES 4 A 240 ASN ASP PRO VAL THR ASN ILE CYS GLN ALA ALA ASP LYS SEQRES 5 A 240 GLN LEU PHE THR LEU VAL GLU TRP ALA LYS ARG ILE PRO SEQRES 6 A 240 HIS PHE SER GLU LEU PRO LEU ASP ASP GLN VAL ILE LEU SEQRES 7 A 240 LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE ALA SER PHE SEQRES 8 A 240 SER HIS ARG SER ILE ALA VAL LYS ASP GLY ILE LEU LEU SEQRES 9 A 240 ALA THR GLY LEU HIS VAL HIS ARG ASN SER ALA HIS SER SEQRES 10 A 240 ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL LEU THR GLU SEQRES 11 A 240 LEU VAL SER LYS MET ARG ASP MET GLN MET ASP LYS THR SEQRES 12 A 240 GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU PHE ASN PRO SEQRES 13 A 240 ASP SER LYS GLY LEU SER ASN PRO ALA GLU VAL GLU ALA SEQRES 14 A 240 LEU ARG GLU LYS VAL TYR ALA SER LEU GLU ALA TYR CYS SEQRES 15 A 240 LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG PHE ALA LYS SEQRES 16 A 240 LEU LEU LEU ARG LEU PRO ALA LEU ARG SER ILE GLY LEU SEQRES 17 A 240 LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS LEU ILE GLY SEQRES 18 A 240 ASP THR PRO ILE ASP THR PHE LEU MET GLU MET LEU GLU SEQRES 19 A 240 ALA PRO HIS GLN MET THR SEQRES 1 B 13 LYS HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP SER SER SEQRES 1 C 240 THR SER SER ALA ASN GLU ASP MET PRO VAL GLU ARG ILE SEQRES 2 C 240 LEU GLU ALA GLU LEU ALA VAL GLU PRO LYS THR GLU THR SEQRES 3 C 240 TYR VAL GLU ALA ASN MET GLY LEU ASN PRO SER SER PRO SEQRES 4 C 240 ASN ASP PRO VAL THR ASN ILE CYS GLN ALA ALA ASP LYS SEQRES 5 C 240 GLN LEU PHE THR LEU VAL GLU TRP ALA LYS ARG ILE PRO SEQRES 6 C 240 HIS PHE SER GLU LEU PRO LEU ASP ASP GLN VAL ILE LEU SEQRES 7 C 240 LEU ARG ALA GLY TRP ASN GLU LEU LEU ILE ALA SER PHE SEQRES 8 C 240 SER HIS ARG SER ILE ALA VAL LYS ASP GLY ILE LEU LEU SEQRES 9 C 240 ALA THR GLY LEU HIS VAL HIS ARG ASN SER ALA HIS SER SEQRES 10 C 240 ALA GLY VAL GLY ALA ILE PHE ASP ARG VAL LEU THR GLU SEQRES 11 C 240 LEU VAL SER LYS MET ARG ASP MET GLN MET ASP LYS THR SEQRES 12 C 240 GLU LEU GLY CYS LEU ARG ALA ILE VAL LEU PHE ASN PRO SEQRES 13 C 240 ASP SER LYS GLY LEU SER ASN PRO ALA GLU VAL GLU ALA SEQRES 14 C 240 LEU ARG GLU LYS VAL TYR ALA SER LEU GLU ALA TYR CYS SEQRES 15 C 240 LYS HIS LYS TYR PRO GLU GLN PRO GLY ARG PHE ALA LYS SEQRES 16 C 240 LEU LEU LEU ARG LEU PRO ALA LEU ARG SER ILE GLY LEU SEQRES 17 C 240 LYS CYS LEU GLU HIS LEU PHE PHE PHE LYS LEU ILE GLY SEQRES 18 C 240 ASP THR PRO ILE ASP THR PHE LEU MET GLU MET LEU GLU SEQRES 19 C 240 ALA PRO HIS GLN MET THR SEQRES 1 D 13 LYS HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP SER SER HET 21P A 1 27 HET 21P C 2 27 HETNAM 21P 4-[2-(1,1,3,3-TETRAMETHYL-2,3-DIHYDRO-1H-1,3- HETNAM 2 21P BENZODISILOL-5-YL)-1,3-DIOXOLAN-2-YL]BENZOIC ACID FORMUL 5 21P 2(C21 H26 O4 SI2) FORMUL 7 HOH *26(H2 O) HELIX 1 1 PRO A 231 VAL A 242 1 12 HELIX 2 2 ASP A 263 ARG A 285 1 23 HELIX 3 3 PRO A 293 SER A 317 1 25 HELIX 4 4 ARG A 334 SER A 339 1 6 HELIX 5 5 VAL A 342 LEU A 353 1 12 HELIX 6 6 LEU A 353 MET A 360 1 8 HELIX 7 7 ASP A 363 PHE A 376 1 14 HELIX 8 8 ASN A 385 TYR A 408 1 24 HELIX 9 9 GLY A 413 LEU A 420 1 8 HELIX 10 10 ARG A 421 GLY A 443 1 23 HELIX 11 11 ASP A 448 LEU A 455 1 8 HELIX 12 12 HIS B 472 ASP B 481 1 10 HELIX 13 13 PRO C 231 VAL C 242 1 12 HELIX 14 14 ASP C 263 ARG C 285 1 23 HELIX 15 15 PRO C 293 ARG C 316 1 24 HELIX 16 16 ARG C 334 SER C 339 1 6 HELIX 17 17 VAL C 342 LEU C 353 1 12 HELIX 18 18 LEU C 353 GLN C 361 1 9 HELIX 19 19 ASP C 363 PHE C 376 1 14 HELIX 20 20 ASN C 385 TYR C 408 1 24 HELIX 21 21 GLY C 413 LEU C 420 1 8 HELIX 22 22 ARG C 421 GLY C 443 1 23 HELIX 23 23 ASP C 448 LEU C 455 1 8 HELIX 24 24 HIS D 472 ASP D 481 1 10 SHEET 1 A 2 GLY A 323 LEU A 325 0 SHEET 2 A 2 HIS A 331 HIS A 333 -1 O VAL A 332 N ILE A 324 SHEET 1 B 2 GLY C 323 LEU C 325 0 SHEET 2 B 2 HIS C 331 HIS C 333 -1 O VAL C 332 N ILE C 324 SITE 1 AC1 15 ILE A 268 ALA A 271 ALA A 272 GLN A 275 SITE 2 AC1 15 TRP A 305 ASN A 306 LEU A 309 ILE A 310 SITE 3 AC1 15 PHE A 313 ARG A 316 ILE A 324 LEU A 326 SITE 4 AC1 15 ALA A 327 CYS A 432 HIS A 435 SITE 1 AC2 13 ILE C 268 ALA C 271 ALA C 272 GLN C 275 SITE 2 AC2 13 ASN C 306 LEU C 309 ILE C 310 PHE C 313 SITE 3 AC2 13 ARG C 316 ALA C 327 VAL C 349 CYS C 432 SITE 4 AC2 13 HIS C 435 CRYST1 64.975 66.850 110.793 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014959 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009026 0.00000