10 20 30 40 50 60 70 80 1RKG - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HORMONE/GROWTH FACTOR RECEPTOR 21-NOV-03 1RKG
TITLE CRYSTAL STRUCTURE OF THE RAT VITAMIN D RECEPTOR LIGAND TITLE 2 BINDING DOMAIN COMPLEXED WITH 2MBISP AND A SYNTHETIC TITLE 3 PEPTIDE CONTAINING THE NR2 BOX OF DRIP 205
COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN; COMPND 5 SYNONYM: VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR COMPND 10 BINDING PROTEIN; COMPND 11 CHAIN: C; COMPND 12 SYNONYM: PBP, PPAR BINDING PROTEIN, THYROID HORMONE COMPND 13 RECEPTOR-ASSOCIATED PROTEIN COMPLEX 220 KDA COMPONENT, COMPND 14 TRAP220, THYROID RECEPTOR INTERACTING PROTEIN 2, TRIP2, COMPND 15 P53 REGULATORY PROTEIN RB18A, VITAMIN D RECEPTOR- COMPND 16 INTERACTING PROTEIN COMPLEX COMPONENT DRIP205, ACTIVATOR- COMPND 17 RECRUITED COFACTOR 205 KDA COMPONENT, ARC205; COMPND 18 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: VDR, NR1I1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL-21(DE3) CODONPLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-29B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES
KEYWDS NUCLEAR RECEPTOR-LIGAND COMPLEX, NUCLEAR RECEPTOR- KEYWDS 2 COACTIVATOR INTERACTIONS, HORMONE/GROWTH FACTOR RECEPTOR KEYWDS 3 COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.L.VANHOOKE,M.M.BENNING,C.B.BAUER,J.W.PIKE,H.F.DELUCA
REVDAT 2 24-FEB-09 1RKG 1 VERSN REVDAT 1 13-APR-04 1RKG 0
JRNL AUTH J.L.VANHOOKE,M.M.BENNING,C.B.BAUER,J.W.PIKE, JRNL AUTH 2 H.F.DELUCA JRNL TITL MOLECULAR STRUCTURE OF THE RAT VITAMIN D RECEPTOR JRNL TITL 2 LIGAND BINDING DOMAIN COMPLEXED WITH JRNL TITL 3 2-CARBON-SUBSTITUTED VITAMIN D(3) HORMONE JRNL TITL 4 ANALOGUES AND A LXXLL-CONTAINING COACTIVATOR JRNL TITL 5 PEPTIDE JRNL REF BIOCHEMISTRY V. 43 4101 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15065852 JRNL DOI 10.1021/BI036056Y
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 22161 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1133 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1460 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 73 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.48000 REMARK 3 B22 (A**2) : 2.72000 REMARK 3 B33 (A**2) : -0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.38000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.156 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.198 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2074 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2808 ; 1.378 ; 1.987 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 250 ; 5.121 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 321 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1528 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1028 ; 0.207 ; 0.200 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): 115 ; 0.139 ; 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): 20 ; 0.154 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.097 ; 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): 1269 ; 0.917 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2054 ; 1.734 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 805 ; 2.779 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 754 ; 4.511 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1RKG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-03. REMARK 100 THE RCSB ID CODE IS RCSB020835.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JAN-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MONTEL OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PROTEUM R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : PROSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22171 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 42.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1RJK REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MOPS, AMMONIUM CITRATE, REMARK 280 ISOPROPANOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 77.22350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.05700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.22350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.05700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE ASYMMETRIC UNIT CONTAINS ONE BIOLOGICAL UNIT. THE REMARK 300 BIOLOGICAL UNIT IS COMPOSED OF ONE MOLECULE OF VDR, ONE LIGAND REMARK 300 MOLECULE (2MBISP), AND ONE MOLECULE OF THE SYNTHETIC PEPTIDE
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: 1960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 154.44700 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LEU A 116 REMARK 465 LYS A 117 REMARK 465 ASP A 118 REMARK 465 SER A 119 REMARK 465 LEU A 120 REMARK 465 ARG A 121 REMARK 465 PRO A 122 REMARK 465 ASP A 160 REMARK 465 GLY A 161 REMARK 465 SER A 162 REMARK 465 THR A 163 REMARK 465 GLY A 164 REMARK 465 SER A 212 REMARK 465 VAL A 213 REMARK 465 THR A 214 REMARK 465 LEU A 215 REMARK 465 ASP A 216 REMARK 465 LEU A 217 REMARK 465 ILE A 422 REMARK 465 SER A 423 REMARK 465 LEU A 424 REMARK 465 VAL A 425 REMARK 465 PRO A 426 REMARK 465 ARG A 427 REMARK 465 GLY A 428 REMARK 465 SER A 429 REMARK 465 MET A 430 REMARK 465 ALA A 431 REMARK 465 ILE A 432 REMARK 465 SER A 433 REMARK 465 ASP A 434 REMARK 465 PRO A 435 REMARK 465 ASN A 436 REMARK 465 SER A 437 REMARK 465 SER A 438 REMARK 465 SER A 439 REMARK 465 VAL A 440 REMARK 465 ASP A 441 REMARK 465 LYS A 442 REMARK 465 LEU A 443 REMARK 465 ALA A 444 REMARK 465 ALA A 445 REMARK 465 ALA A 446 REMARK 465 LEU A 447 REMARK 465 GLU A 448 REMARK 465 HIS A 449 REMARK 465 HIS A 450 REMARK 465 HIS A 451 REMARK 465 HIS A 452 REMARK 465 HIS A 453 REMARK 465 HIS A 454 REMARK 465 LYS C 625 REMARK 465 ASN C 637
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 123 CG CD CE NZ REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 SER A 218 CB OG REMARK 470 GLN A 403 CG CD OE1 NE2 REMARK 470 GLU A 421 CB CG CD OE1 OE2 REMARK 470 ASN C 626 CG OD1 ND2 REMARK 470 ASP C 636 CG OD1 OD2
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 ASP A 228 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 292 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 344 CB - CG - OD2 ANGL. DEV. = 5.5 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 LEU A 220 51.11 74.62 REMARK 500 ASP A 279 23.43 -142.28 REMARK 500 TYR A 289 43.92 -108.30 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 A 607 DISTANCE = 6.43 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE VD1 A 500
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RJK RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH 2MD [2-METHYLENE-19-NOR-(20S)- REMARK 900 1ALPHA,25-DIHYDROXYVITAMIN D3] REMARK 900 RELATED ID: 1RK3 RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH 1ALPHA,25-DIHYDROXYVITAMIN D3 REMARK 900 RELATED ID: 1RKH RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH 2AM20R [2ALPHA-METHYL-19-NOR-1, REMARK 900 25-DIHYDROXYVITAMIN D3]
DBREF 1RKG A 116 423 UNP P13053 VDR_RAT 116 423 DBREF 1RKG C 625 637 UNP Q15648 PPRB_HUMAN 640 652
SEQADV 1RKG A UNP P13053 SER 165 DELETION SEQADV 1RKG A UNP P13053 TYR 166 DELETION SEQADV 1RKG A UNP P13053 SER 167 DELETION SEQADV 1RKG A UNP P13053 PRO 168 DELETION SEQADV 1RKG A UNP P13053 ARG 169 DELETION SEQADV 1RKG A UNP P13053 PRO 170 DELETION SEQADV 1RKG A UNP P13053 THR 171 DELETION SEQADV 1RKG A UNP P13053 LEU 172 DELETION SEQADV 1RKG A UNP P13053 SER 173 DELETION SEQADV 1RKG A UNP P13053 PHE 174 DELETION SEQADV 1RKG A UNP P13053 SER 175 DELETION SEQADV 1RKG A UNP P13053 GLY 176 DELETION SEQADV 1RKG A UNP P13053 ASN 177 DELETION SEQADV 1RKG A UNP P13053 SER 178 DELETION SEQADV 1RKG A UNP P13053 SER 179 DELETION SEQADV 1RKG A UNP P13053 SER 180 DELETION SEQADV 1RKG A UNP P13053 SER 181 DELETION SEQADV 1RKG A UNP P13053 SER 182 DELETION SEQADV 1RKG A UNP P13053 SER 183 DELETION SEQADV 1RKG A UNP P13053 ASP 184 DELETION SEQADV 1RKG A UNP P13053 LEU 185 DELETION SEQADV 1RKG A UNP P13053 TYR 186 DELETION SEQADV 1RKG A UNP P13053 THR 187 DELETION SEQADV 1RKG A UNP P13053 THR 188 DELETION SEQADV 1RKG A UNP P13053 SER 189 DELETION SEQADV 1RKG A UNP P13053 LEU 190 DELETION SEQADV 1RKG A UNP P13053 ASP 191 DELETION SEQADV 1RKG A UNP P13053 MET 192 DELETION SEQADV 1RKG A UNP P13053 MET 193 DELETION SEQADV 1RKG A UNP P13053 GLU 194 DELETION SEQADV 1RKG A UNP P13053 PRO 195 DELETION SEQADV 1RKG A UNP P13053 SER 196 DELETION SEQADV 1RKG A UNP P13053 GLY 197 DELETION SEQADV 1RKG A UNP P13053 PHE 198 DELETION SEQADV 1RKG A UNP P13053 SER 199 DELETION SEQADV 1RKG A UNP P13053 ASN 200 DELETION SEQADV 1RKG A UNP P13053 LEU 201 DELETION SEQADV 1RKG A UNP P13053 ASP 202 DELETION SEQADV 1RKG A UNP P13053 LEU 203 DELETION SEQADV 1RKG A UNP P13053 ASN 204 DELETION SEQADV 1RKG A UNP P13053 GLY 205 DELETION SEQADV 1RKG A UNP P13053 GLU 206 DELETION SEQADV 1RKG A UNP P13053 ASP 207 DELETION SEQADV 1RKG A UNP P13053 SER 208 DELETION SEQADV 1RKG A UNP P13053 ASP 209 DELETION SEQADV 1RKG A UNP P13053 ASP 210 DELETION SEQADV 1RKG A UNP P13053 PRO 211 DELETION SEQADV 1RKG LEU A 424 UNP P13053 CLONING ARTIFACT SEQADV 1RKG VAL A 425 UNP P13053 CLONING ARTIFACT SEQADV 1RKG PRO A 426 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ARG A 427 UNP P13053 CLONING ARTIFACT SEQADV 1RKG GLY A 428 UNP P13053 CLONING ARTIFACT SEQADV 1RKG SER A 429 UNP P13053 CLONING ARTIFACT SEQADV 1RKG MET A 430 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ALA A 431 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ILE A 432 UNP P13053 CLONING ARTIFACT SEQADV 1RKG SER A 433 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ASP A 434 UNP P13053 CLONING ARTIFACT SEQADV 1RKG PRO A 435 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ASN A 436 UNP P13053 CLONING ARTIFACT SEQADV 1RKG SER A 437 UNP P13053 CLONING ARTIFACT SEQADV 1RKG SER A 438 UNP P13053 CLONING ARTIFACT SEQADV 1RKG SER A 439 UNP P13053 CLONING ARTIFACT SEQADV 1RKG VAL A 440 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ASP A 441 UNP P13053 CLONING ARTIFACT SEQADV 1RKG LYS A 442 UNP P13053 CLONING ARTIFACT SEQADV 1RKG LEU A 443 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ALA A 444 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ALA A 445 UNP P13053 CLONING ARTIFACT SEQADV 1RKG ALA A 446 UNP P13053 CLONING ARTIFACT SEQADV 1RKG LEU A 447 UNP P13053 CLONING ARTIFACT SEQADV 1RKG GLU A 448 UNP P13053 CLONING ARTIFACT SEQADV 1RKG HIS A 449 UNP P13053 EXPRESSION TAG SEQADV 1RKG HIS A 450 UNP P13053 EXPRESSION TAG SEQADV 1RKG HIS A 451 UNP P13053 EXPRESSION TAG SEQADV 1RKG HIS A 452 UNP P13053 EXPRESSION TAG SEQADV 1RKG HIS A 453 UNP P13053 EXPRESSION TAG SEQADV 1RKG HIS A 454 UNP P13053 EXPRESSION TAG
SEQRES 1 A 292 LEU LYS ASP SER LEU ARG PRO LYS LEU SER GLU GLU GLN SEQRES 2 A 292 GLN HIS ILE ILE ALA ILE LEU LEU ASP ALA HIS HIS LYS SEQRES 3 A 292 THR TYR ASP PRO THR TYR ALA ASP PHE ARG ASP PHE ARG SEQRES 4 A 292 PRO PRO VAL ARG MET ASP GLY SER THR GLY SER VAL THR SEQRES 5 A 292 LEU ASP LEU SER PRO LEU SER MET LEU PRO HIS LEU ALA SEQRES 6 A 292 ASP LEU VAL SER TYR SER ILE GLN LYS VAL ILE GLY PHE SEQRES 7 A 292 ALA LYS MET ILE PRO GLY PHE ARG ASP LEU THR SER ASP SEQRES 8 A 292 ASP GLN ILE VAL LEU LEU LYS SER SER ALA ILE GLU VAL SEQRES 9 A 292 ILE MET LEU ARG SER ASN GLN SER PHE THR MET ASP ASP SEQRES 10 A 292 MET SER TRP ASP CYS GLY SER GLN ASP TYR LYS TYR ASP SEQRES 11 A 292 VAL THR ASP VAL SER LYS ALA GLY HIS THR LEU GLU LEU SEQRES 12 A 292 ILE GLU PRO LEU ILE LYS PHE GLN VAL GLY LEU LYS LYS SEQRES 13 A 292 LEU ASN LEU HIS GLU GLU GLU HIS VAL LEU LEU MET ALA SEQRES 14 A 292 ILE CYS ILE VAL SER PRO ASP ARG PRO GLY VAL GLN ASP SEQRES 15 A 292 ALA LYS LEU VAL GLU ALA ILE GLN ASP ARG LEU SER ASN SEQRES 16 A 292 THR LEU GLN THR TYR ILE ARG CYS ARG HIS PRO PRO PRO SEQRES 17 A 292 GLY SER HIS GLN LEU TYR ALA LYS MET ILE GLN LYS LEU SEQRES 18 A 292 ALA ASP LEU ARG SER LEU ASN GLU GLU HIS SER LYS GLN SEQRES 19 A 292 TYR ARG SER LEU SER PHE GLN PRO GLU ASN SER MET LYS SEQRES 20 A 292 LEU THR PRO LEU VAL LEU GLU VAL PHE GLY ASN GLU ILE SEQRES 21 A 292 SER LEU VAL PRO ARG GLY SER MET ALA ILE SER ASP PRO SEQRES 22 A 292 ASN SER SER SER VAL ASP LYS LEU ALA ALA ALA LEU GLU SEQRES 23 A 292 HIS HIS HIS HIS HIS HIS SEQRES 1 C 13 LYS ASN HIS PRO MET LEU MET ASN LEU LEU LYS ASP ASN
HET VD1 A 500 25
HETNAM VD1 5-{2-[1-(1-METHYL-PROPYL)-7A-METHYL-OCTAHYDRO-INDEN-4- HETNAM 2 VD1 YLIDENE]-ETHYLIDENE}-2-METHYLENE-CYCLOHEXANE-1,3-DIOL
HETSYN VD1 1-ALPHA-HYDROXY-2-METHYLENE-19-NOR-(20S)- HETSYN 2 VD1 BISHOMOPREGNACALCIFEROL; 2MBISP
FORMUL 3 VD1 C23 H36 O2 FORMUL 4 HOH *125(H2 O)
HELIX 1 1 SER A 125 TYR A 143 1 19 HELIX 2 2 TYR A 147 PHE A 153 5 7 HELIX 3 3 MET A 222 LYS A 242 1 21 HELIX 4 4 GLY A 246 LEU A 250 5 5 HELIX 5 5 THR A 251 SER A 271 1 21 HELIX 6 6 SER A 286 ASP A 288 5 3 HELIX 7 7 ASP A 292 LYS A 298 1 7 HELIX 8 8 THR A 302 LEU A 319 1 18 HELIX 9 9 HIS A 322 VAL A 335 1 14 HELIX 10 10 ASP A 344 HIS A 367 1 24 HELIX 11 11 GLN A 374 GLN A 403 1 30 HELIX 12 12 GLN A 403 MET A 408 1 6 HELIX 13 13 THR A 411 ASN A 420 1 10 HELIX 14 14 HIS C 627 LYS C 635 1 9
SHEET 1 A 3 PHE A 275 THR A 276 0 SHEET 2 A 3 SER A 281 ASP A 283 -1 O SER A 281 N THR A 276 SHEET 3 A 3 LYS A 290 TYR A 291 -1 O TYR A 291 N TRP A 282
CISPEP 1 PRO A 369 PRO A 370 0 6.20
SITE 1 AC1 8 TYR A 143 VAL A 230 SER A 233 ARG A 270 SITE 2 AC1 8 SER A 271 SER A 274 TRP A 282 CYS A 284
CRYST1 154.447 44.114 41.860 90.00 96.62 90.00 C 1 2 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 0.006475 0.000000 0.000751 0.00000
SCALE2 0.000000 0.022669 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024049 0.00000