PDB Short entry for 1RKH HEADER HORMONE/GROWTH FACTOR RECEPTOR 21-NOV-03 1RKH TITLE CRYSTAL STRUCTURE OF THE RAT VITAMIN D RECEPTOR LIGAND BINDING DOMAIN TITLE 2 COMPLEXED WITH 2AM20R AND A SYNTHETIC PEPTIDE CONTAINING THE NR2 BOX TITLE 3 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 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 KEYWDS NUCLEAR RECEPTOR-LIGAND 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 1RKH 1 REMARK SEQADV REVDAT 3 11-OCT-17 1RKH 1 REMARK REVDAT 2 24-FEB-09 1RKH 1 VERSN REVDAT 1 13-APR-04 1RKH 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. 2.28 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 11278 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 554 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 573 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 28 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1994 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.40000 REMARK 3 B22 (A**2) : 3.68000 REMARK 3 B33 (A**2) : -0.41000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.58000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.407 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.155 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.451 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2067 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2803 ; 1.460 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 250 ; 5.528 ; 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): 322 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1515 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 954 ; 0.213 ; 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): 82 ; 0.129 ; 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): 21 ; 0.190 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.016 ; 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): 1267 ; 0.758 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2051 ; 1.465 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 800 ; 2.512 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 752 ; 4.124 ; 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 1RKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020836. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-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 : LSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11285 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 40.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.14900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 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 (%): 37.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 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 77.40000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.14550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.40000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.14550 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 (2AM20R), 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: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 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: 5870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 154.80000 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 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 SER A 218 CB OG REMARK 470 ARG A 364 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 403 CG CD OE1 NE2 REMARK 470 GLU A 421 CG CD OE1 OE2 REMARK 470 LYS C 625 CG CD CE NZ REMARK 470 ASN C 626 CB CG OD1 ND2 REMARK 470 LYS C 635 CG CD CE NZ 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. = 6.2 DEGREES REMARK 500 ASP A 344 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 LEU A 400 CA - CB - CG ANGL. DEV. = 13.9 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 CYS A 284 43.52 -103.51 REMARK 500 TYR A 289 46.14 -105.64 REMARK 500 GLN A 343 -72.13 -91.22 REMARK 500 ASN A 420 55.78 -148.67 REMARK 500 ASN C 626 87.93 72.80 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 VD2 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)-1ALPHA,25- REMARK 900 DIHYDROXYVITAMIN D3] 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 DBREF 1RKH A 116 423 UNP P13053 VDR_RAT 116 423 DBREF 1RKH C 625 637 UNP Q15648 PPRB_HUMAN 640 652 SEQADV 1RKH A UNP P13053 SER 165 DELETION SEQADV 1RKH A UNP P13053 TYR 166 DELETION SEQADV 1RKH A UNP P13053 SER 167 DELETION SEQADV 1RKH A UNP P13053 PRO 168 DELETION SEQADV 1RKH A UNP P13053 ARG 169 DELETION SEQADV 1RKH A UNP P13053 PRO 170 DELETION SEQADV 1RKH A UNP P13053 THR 171 DELETION SEQADV 1RKH A UNP P13053 LEU 172 DELETION SEQADV 1RKH A UNP P13053 SER 173 DELETION SEQADV 1RKH A UNP P13053 PHE 174 DELETION SEQADV 1RKH A UNP P13053 SER 175 DELETION SEQADV 1RKH A UNP P13053 GLY 176 DELETION SEQADV 1RKH A UNP P13053 ASN 177 DELETION SEQADV 1RKH A UNP P13053 SER 178 DELETION SEQADV 1RKH A UNP P13053 SER 179 DELETION SEQADV 1RKH A UNP P13053 SER 180 DELETION SEQADV 1RKH A UNP P13053 SER 181 DELETION SEQADV 1RKH A UNP P13053 SER 182 DELETION SEQADV 1RKH A UNP P13053 SER 183 DELETION SEQADV 1RKH A UNP P13053 ASP 184 DELETION SEQADV 1RKH A UNP P13053 LEU 185 DELETION SEQADV 1RKH A UNP P13053 TYR 186 DELETION SEQADV 1RKH A UNP P13053 THR 187 DELETION SEQADV 1RKH A UNP P13053 THR 188 DELETION SEQADV 1RKH A UNP P13053 SER 189 DELETION SEQADV 1RKH A UNP P13053 LEU 190 DELETION SEQADV 1RKH A UNP P13053 ASP 191 DELETION SEQADV 1RKH A UNP P13053 MET 192 DELETION SEQADV 1RKH A UNP P13053 MET 193 DELETION SEQADV 1RKH A UNP P13053 GLU 194 DELETION SEQADV 1RKH A UNP P13053 PRO 195 DELETION SEQADV 1RKH A UNP P13053 SER 196 DELETION SEQADV 1RKH A UNP P13053 GLY 197 DELETION SEQADV 1RKH A UNP P13053 PHE 198 DELETION SEQADV 1RKH A UNP P13053 SER 199 DELETION SEQADV 1RKH A UNP P13053 ASN 200 DELETION SEQADV 1RKH A UNP P13053 LEU 201 DELETION SEQADV 1RKH A UNP P13053 ASP 202 DELETION SEQADV 1RKH A UNP P13053 LEU 203 DELETION SEQADV 1RKH A UNP P13053 ASN 204 DELETION SEQADV 1RKH A UNP P13053 GLY 205 DELETION SEQADV 1RKH A UNP P13053 GLU 206 DELETION SEQADV 1RKH A UNP P13053 ASP 207 DELETION SEQADV 1RKH A UNP P13053 SER 208 DELETION SEQADV 1RKH A UNP P13053 ASP 209 DELETION SEQADV 1RKH A UNP P13053 ASP 210 DELETION SEQADV 1RKH A UNP P13053 PRO 211 DELETION SEQADV 1RKH LEU A 424 UNP P13053 CLONING ARTIFACT SEQADV 1RKH VAL A 425 UNP P13053 CLONING ARTIFACT SEQADV 1RKH PRO A 426 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ARG A 427 UNP P13053 CLONING ARTIFACT SEQADV 1RKH GLY A 428 UNP P13053 CLONING ARTIFACT SEQADV 1RKH SER A 429 UNP P13053 CLONING ARTIFACT SEQADV 1RKH MET A 430 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ALA A 431 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ILE A 432 UNP P13053 CLONING ARTIFACT SEQADV 1RKH SER A 433 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ASP A 434 UNP P13053 CLONING ARTIFACT SEQADV 1RKH PRO A 435 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ASN A 436 UNP P13053 CLONING ARTIFACT SEQADV 1RKH SER A 437 UNP P13053 CLONING ARTIFACT SEQADV 1RKH SER A 438 UNP P13053 CLONING ARTIFACT SEQADV 1RKH SER A 439 UNP P13053 CLONING ARTIFACT SEQADV 1RKH VAL A 440 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ASP A 441 UNP P13053 CLONING ARTIFACT SEQADV 1RKH LYS A 442 UNP P13053 CLONING ARTIFACT SEQADV 1RKH LEU A 443 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ALA A 444 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ALA A 445 UNP P13053 CLONING ARTIFACT SEQADV 1RKH ALA A 446 UNP P13053 CLONING ARTIFACT SEQADV 1RKH LEU A 447 UNP P13053 CLONING ARTIFACT SEQADV 1RKH GLU A 448 UNP P13053 CLONING ARTIFACT SEQADV 1RKH HIS A 449 UNP P13053 EXPRESSION TAG SEQADV 1RKH HIS A 450 UNP P13053 EXPRESSION TAG SEQADV 1RKH HIS A 451 UNP P13053 EXPRESSION TAG SEQADV 1RKH HIS A 452 UNP P13053 EXPRESSION TAG SEQADV 1RKH HIS A 453 UNP P13053 EXPRESSION TAG SEQADV 1RKH 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 VD2 A 500 30 HETNAM VD2 5-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL- HETNAM 2 VD2 OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-2-METHYL- HETNAM 3 VD2 CYCLOHEXANE-1,3-DIOL HETSYN VD2 2-ALPHA-METHYL-19-NOR-1,25-DIHYDROXYVITAMIN D3; 2AM20R FORMUL 3 VD2 C27 H46 O3 FORMUL 4 HOH *68(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 ASP A 292 LYS A 298 1 7 HELIX 7 7 THR A 302 LYS A 318 1 17 HELIX 8 8 HIS A 322 VAL A 335 1 14 HELIX 9 9 ASP A 344 HIS A 367 1 24 HELIX 10 10 GLN A 374 GLN A 403 1 30 HELIX 11 11 GLN A 403 MET A 408 1 6 HELIX 12 12 THR A 411 GLY A 419 1 9 HELIX 13 13 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 3.15 SITE 1 AC1 11 TYR A 143 VAL A 230 SER A 233 ARG A 270 SITE 2 AC1 11 SER A 271 SER A 274 TRP A 282 CYS A 284 SITE 3 AC1 11 HIS A 301 LEU A 305 HIS A 393 CRYST1 154.800 42.291 41.788 90.00 96.15 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 0.006460 0.000000 0.000696 0.00000 SCALE2 0.000000 0.023646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024069 0.00000