HEADER HORMONE/GROWTH FACTOR RECEPTOR 19-NOV-03 1RJK
TITLE CRYSTAL STRUCTURE OF THE RAT VITAMIN D RECEPTOR LIGAND BINDING DOMAIN
TITLE 2 COMPLEXED WITH 2MD AND A SYNTHETIC PEPTIDE CONTAINING THE NR2 BOX OF
TITLE 3 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 BINDING PROTEIN;
COMPND 10 CHAIN: C;
COMPND 11 FRAGMENT: DRIP 205 NR2 BOX PEPTIDE;
COMPND 12 SYNONYM: PBP, PPAR BINDING PROTEIN, THYROID HORMONE RECEPTOR-
COMPND 13 ASSOCIATED PROTEIN COMPLEX 220 KDA COMPONENT, TRAP220, THYROID
COMPND 14 RECEPTOR INTERACTING PROTEIN 2, TRIP2, P53 REGULATORY PROTEIN RB18A,
COMPND 15 VITAMIN D RECEPTOR-INTERACTING PROTEIN COMPLEX COMPONENT DRIP205,
COMPND 16 ACTIVATOR-RECRUITED COFACTOR 205 KDA COMPONENT, ARC205;
COMPND 17 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;
SOURCE 13 OTHER_DETAILS: SYNTHESIZED AT UW-MADISON BIOTECHNOLOGY CENTER
KEYWDS NUCLEAR RECEPTOR-SUPERAGONIST COMPLEX, NUCLEAR RECEPTOR-COACTIVATOR
KEYWDS 2 INTERACTIONS, HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR J.L.VANHOOKE,M.M.BENNING,C.B.BAUER,J.W.PIKE,H.F.DELUCA
REVDAT 4 23-AUG-23 1RJK 1 COMPND REMARK SEQADV HETNAM
REVDAT 3 11-OCT-17 1RJK 1 REMARK
REVDAT 2 24-FEB-09 1RJK 1 VERSN
REVDAT 1 13-APR-04 1RJK 0
JRNL AUTH J.L.VANHOOKE,M.M.BENNING,C.B.BAUER,J.W.PIKE,H.F.DELUCA
JRNL TITL MOLECULAR STRUCTURE OF THE RAT VITAMIN D RECEPTOR LIGAND
JRNL TITL 2 BINDING DOMAIN COMPLEXED WITH 2-CARBON-SUBSTITUTED VITAMIN
JRNL TITL 3 D(3) HORMONE ANALOGUES AND A LXXLL-CONTAINING COACTIVATOR
JRNL TITL 4 PEPTIDE
JRNL REF BIOCHEMISTRY V. 43 4101 2004
JRNL REFN ISSN 0006-2960
JRNL PMID 15065852
JRNL DOI 10.1021/BI036056Y
REMARK 2
REMARK 2 RESOLUTION. 1.99 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.1.24
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) : 1.99
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 18937
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) : 0.188
REMARK 3 R VALUE (WORKING SET) : 0.185
REMARK 3 FREE R VALUE : 0.244
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 977
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) : 1.99
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05
REMARK 3 REFLECTION IN BIN (WORKING SET) : 1218
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : 0.2320
REMARK 3 BIN FREE R VALUE SET COUNT : 74
REMARK 3 BIN FREE R VALUE : 0.2930
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1987
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 30
REMARK 3 SOLVENT ATOMS : 131
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.93
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -2.94000
REMARK 3 B22 (A**2) : 3.45000
REMARK 3 B33 (A**2) : -0.61000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : -0.48000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.180
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.172
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.968
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2063 ; 0.015 ; 0.021
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2794 ; 1.394 ; 1.990
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 247 ; 4.895 ; 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): 320 ; 0.089 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1512 ; 0.006 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1044 ; 0.206 ; 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): 125 ; 0.133 ; 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 ; 0.185 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.089 ; 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): 1253 ; 0.870 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2031 ; 1.637 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 810 ; 2.573 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 763 ; 4.184 ; 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 : 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 1RJK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-03.
REMARK 100 THE DEPOSITION ID IS D_1000020806.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 27-OCT-02
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 : LSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18940
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990
REMARK 200 RESOLUTION RANGE LOW (A) : 33.070
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0
REMARK 200 DATA REDUNDANCY : 4.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.05100
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.08
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.16100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500
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: PDB ENTRY 1DB1
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.93
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MOPS, AMMONIUM CITRATE,
REMARK 280 ISOPROPANOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE
REMARK 280 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 77.30000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.64600
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.30000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.64600
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 (VDZ), 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: 2070 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 11700 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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: 5720 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 21820 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 154.60000
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 SER A 218
REMARK 465 GLU A 421
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 ASP C 636
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 GLN A 403 CG CD OE1 NE2
REMARK 470 LYS C 625 CB CG CD CE NZ
REMARK 470 ASN C 626 CG OD1 ND2
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 292 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES
REMARK 500 ASP A 385 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES
REMARK 500 LEU A 400 CA - CB - CG ANGL. DEV. = 17.6 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 LEU A 220 49.03 77.63
REMARK 500 TYR A 289 44.76 -108.66
REMARK 500 ASN C 626 107.94 79.01
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 VDZ A 500
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1RK3 RELATED DB: PDB
REMARK 900 SAME PROTEIN COMPLEXED WITH 1ALPHA,25-DIHYDROXYVITAMIN D3
REMARK 900 RELATED ID: 1RKG RELATED DB: PDB
REMARK 900 SAME PROTEIN COMPLEXED WITH 2MBISP [1ALPHA-HYDROXY-2-METHYLENE-19-
REMARK 900 NOR-(20S)-BISHOMOPREGNACALCIFEROL]
REMARK 900 RELATED ID: 1RKH RELATED DB: PDB
REMARK 900 SAME PROTEIN COMPLEXED WITH 2AM20R [2ALPHA-METHYL-19-NOR-1,25-
REMARK 900 DIHYDROXYVITAMIN D3]
DBREF 1RJK A 116 423 UNP P13053 VDR_RAT 116 423
DBREF 1RJK C 625 637 UNP Q15648 PPRB_HUMAN 640 652
SEQADV 1RJK A UNP P13053 SER 165 DELETION
SEQADV 1RJK A UNP P13053 TYR 166 DELETION
SEQADV 1RJK A UNP P13053 SER 167 DELETION
SEQADV 1RJK A UNP P13053 PRO 168 DELETION
SEQADV 1RJK A UNP P13053 ARG 169 DELETION
SEQADV 1RJK A UNP P13053 PRO 170 DELETION
SEQADV 1RJK A UNP P13053 THR 171 DELETION
SEQADV 1RJK A UNP P13053 LEU 172 DELETION
SEQADV 1RJK A UNP P13053 SER 173 DELETION
SEQADV 1RJK A UNP P13053 PHE 174 DELETION
SEQADV 1RJK A UNP P13053 SER 175 DELETION
SEQADV 1RJK A UNP P13053 GLY 176 DELETION
SEQADV 1RJK A UNP P13053 ASN 177 DELETION
SEQADV 1RJK A UNP P13053 SER 178 DELETION
SEQADV 1RJK A UNP P13053 SER 179 DELETION
SEQADV 1RJK A UNP P13053 SER 180 DELETION
SEQADV 1RJK A UNP P13053 SER 181 DELETION
SEQADV 1RJK A UNP P13053 SER 182 DELETION
SEQADV 1RJK A UNP P13053 SER 183 DELETION
SEQADV 1RJK A UNP P13053 ASP 184 DELETION
SEQADV 1RJK A UNP P13053 LEU 185 DELETION
SEQADV 1RJK A UNP P13053 TYR 186 DELETION
SEQADV 1RJK A UNP P13053 THR 187 DELETION
SEQADV 1RJK A UNP P13053 THR 188 DELETION
SEQADV 1RJK A UNP P13053 SER 189 DELETION
SEQADV 1RJK A UNP P13053 LEU 190 DELETION
SEQADV 1RJK A UNP P13053 ASP 191 DELETION
SEQADV 1RJK A UNP P13053 MET 192 DELETION
SEQADV 1RJK A UNP P13053 MET 193 DELETION
SEQADV 1RJK A UNP P13053 GLU 194 DELETION
SEQADV 1RJK A UNP P13053 PRO 195 DELETION
SEQADV 1RJK A UNP P13053 SER 196 DELETION
SEQADV 1RJK A UNP P13053 GLY 197 DELETION
SEQADV 1RJK A UNP P13053 PHE 198 DELETION
SEQADV 1RJK A UNP P13053 SER 199 DELETION
SEQADV 1RJK A UNP P13053 ASN 200 DELETION
SEQADV 1RJK A UNP P13053 LEU 201 DELETION
SEQADV 1RJK A UNP P13053 ASP 202 DELETION
SEQADV 1RJK A UNP P13053 LEU 203 DELETION
SEQADV 1RJK A UNP P13053 ASN 204 DELETION
SEQADV 1RJK A UNP P13053 GLY 205 DELETION
SEQADV 1RJK A UNP P13053 GLU 206 DELETION
SEQADV 1RJK A UNP P13053 ASP 207 DELETION
SEQADV 1RJK A UNP P13053 SER 208 DELETION
SEQADV 1RJK A UNP P13053 ASP 209 DELETION
SEQADV 1RJK A UNP P13053 ASP 210 DELETION
SEQADV 1RJK A UNP P13053 PRO 211 DELETION
SEQADV 1RJK LEU A 424 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK VAL A 425 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK PRO A 426 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ARG A 427 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK GLY A 428 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK SER A 429 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK MET A 430 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ALA A 431 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ILE A 432 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK SER A 433 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ASP A 434 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK PRO A 435 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ASN A 436 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK SER A 437 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK SER A 438 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK SER A 439 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK VAL A 440 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ASP A 441 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK LYS A 442 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK LEU A 443 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ALA A 444 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ALA A 445 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK ALA A 446 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK LEU A 447 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK GLU A 448 UNP P13053 CLONING ARTIFACT
SEQADV 1RJK HIS A 449 UNP P13053 EXPRESSION TAG
SEQADV 1RJK HIS A 450 UNP P13053 EXPRESSION TAG
SEQADV 1RJK HIS A 451 UNP P13053 EXPRESSION TAG
SEQADV 1RJK HIS A 452 UNP P13053 EXPRESSION TAG
SEQADV 1RJK HIS A 453 UNP P13053 EXPRESSION TAG
SEQADV 1RJK 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 VDZ A 500 30
HETNAM VDZ 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-
HETNAM 2 VDZ OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYLENE-
HETNAM 3 VDZ CYCLOHEXANE-1,3-DIO L
HETSYN VDZ 2-METHYLENE-19-NOR-(20S)-1ALPHA,25-DIHYDROXY-VITAMIN
HETSYN 2 VDZ D3; 2MD
FORMUL 3 VDZ C27 H44 O3
FORMUL 4 HOH *131(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 MET A 243 1 22
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 GLY A 419 1 9
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 3.59
SITE 1 AC1 10 TYR A 143 LEU A 223 SER A 233 ARG A 270
SITE 2 AC1 10 SER A 271 SER A 274 TRP A 282 CYS A 284
SITE 3 AC1 10 HIS A 301 HIS A 393
CRYST1 154.600 43.292 41.848 90.00 96.07 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 0.006468 0.000000 0.000688 0.00000
SCALE2 0.000000 0.023099 0.000000 0.00000
SCALE3 0.000000 0.000000 0.024031 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
