HEADER TRANSCRIPTION 08-APR-14 3WT6 TITLE A MIXED POPULATION OF ANTAGONIST AND AGONIST BINDING CONFORMERS IN A TITLE 2 SINGLE CRYSTAL EXPLAINS PARTIAL AGONISM AGAINST VITAMIN D RECEPTOR: TITLE 3 ACTIVE VITAMIN D ANALOGUES WITH 22R-ALKYL GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN, UNP RESIDUES 116-164, 212-423; COMPND 5 SYNONYM: VDR, 1,25-DIHYDROXYVITAMIN D3 RECEPTOR, NUCLEAR RECEPTOR COMPND 6 SUBFAMILY 1 GROUP I MEMBER 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1; COMPND 10 CHAIN: C; COMPND 11 FRAGMENT: DRIP205 NR2 BOX PEPTIDE, UNP RESIDUES 640-652; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: VDR, NR1I1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS TRANSCRIPTION, VITAMIN D3, VDRE, RXR, CO-FACTORS, NUCLEAR EXPDTA X-RAY DIFFRACTION AUTHOR Y.ANAMI,T.ITOH,K.YAMAMOTO REVDAT 3 20-MAR-24 3WT6 1 REMARK SEQADV REVDAT 2 22-NOV-17 3WT6 1 REMARK REVDAT 1 11-JUN-14 3WT6 0 JRNL AUTH Y.ANAMI,T.ITOH,D.EGAWA,N.YOSHIMOTO,K.YAMAMOTO JRNL TITL A MIXED POPULATION OF ANTAGONIST AND AGONIST BINDING JRNL TITL 2 CONFORMERS IN A SINGLE CRYSTAL EXPLAINS PARTIAL AGONISM JRNL TITL 3 AGAINST VITAMIN D RECEPTOR: ACTIVE VITAMIN D ANALOGUES WITH JRNL TITL 4 22R-ALKYL GROUP. JRNL REF J.MED.CHEM. V. 57 4351 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 24742174 JRNL DOI 10.1021/JM500392T REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 16191 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 870 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1224 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.2360 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1993 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 58 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.41000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : 0.68000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.215 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.166 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.678 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 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): 2124 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2104 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2884 ; 1.923 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4863 ; 3.480 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 251 ; 5.305 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;38.166 ;24.556 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 380 ;16.598 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;14.585 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 333 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2291 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 455 ; 0.025 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 123 A 419 REMARK 3 ORIGIN FOR THE GROUP (A): 14.6856 0.0669 56.4998 REMARK 3 T TENSOR REMARK 3 T11: 0.0625 T22: 0.0567 REMARK 3 T33: 0.0445 T12: -0.0113 REMARK 3 T13: 0.0335 T23: -0.0197 REMARK 3 L TENSOR REMARK 3 L11: 0.4603 L22: 0.2367 REMARK 3 L33: 0.1258 L12: 0.1697 REMARK 3 L13: 0.0454 L23: -0.1259 REMARK 3 S TENSOR REMARK 3 S11: 0.0537 S12: -0.0310 S13: 0.0851 REMARK 3 S21: 0.0342 S22: -0.0485 S23: 0.0496 REMARK 3 S31: 0.0061 S32: 0.0186 S33: -0.0052 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 625 C 635 REMARK 3 ORIGIN FOR THE GROUP (A): 8.9106 -10.8219 41.5366 REMARK 3 T TENSOR REMARK 3 T11: 0.0497 T22: 0.0829 REMARK 3 T33: 0.0674 T12: 0.0557 REMARK 3 T13: -0.0269 T23: -0.0598 REMARK 3 L TENSOR REMARK 3 L11: 15.8055 L22: 4.5636 REMARK 3 L33: 4.0531 L12: 6.3539 REMARK 3 L13: -1.1405 L23: -3.2825 REMARK 3 S TENSOR REMARK 3 S11: 0.1178 S12: 0.1614 S13: -0.4014 REMARK 3 S21: -0.1290 S22: -0.1376 S23: -0.1507 REMARK 3 S31: 0.2354 S32: 0.2571 S33: 0.0198 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 501 A 501 REMARK 3 ORIGIN FOR THE GROUP (A): 6.3457 3.2075 58.0546 REMARK 3 T TENSOR REMARK 3 T11: 0.0393 T22: 0.0859 REMARK 3 T33: 0.1600 T12: -0.0057 REMARK 3 T13: 0.0479 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 4.0273 L22: 11.2679 REMARK 3 L33: 1.5124 L12: -0.7565 REMARK 3 L13: 1.6623 L23: -3.2749 REMARK 3 S TENSOR REMARK 3 S11: 0.0655 S12: -0.2103 S13: 0.2539 REMARK 3 S21: 0.4333 S22: 0.0176 S23: 0.3305 REMARK 3 S31: -0.0966 S32: -0.1003 S33: -0.0831 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 601 A 656 REMARK 3 RESIDUE RANGE : C 701 C 702 REMARK 3 ORIGIN FOR THE GROUP (A): 20.2331 -1.2684 50.7768 REMARK 3 T TENSOR REMARK 3 T11: 0.0561 T22: 0.0479 REMARK 3 T33: 0.0140 T12: 0.0245 REMARK 3 T13: 0.0024 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 1.1254 L22: 0.6278 REMARK 3 L33: 0.2369 L12: 0.2142 REMARK 3 L13: 0.1623 L23: -0.0332 REMARK 3 S TENSOR REMARK 3 S11: -0.0049 S12: 0.0166 S13: 0.1151 REMARK 3 S21: 0.0400 S22: -0.0161 S23: 0.0536 REMARK 3 S31: 0.0333 S32: 0.0476 S33: 0.0211 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3WT6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000096760. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17061 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLECULAR REPLACEMENT REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOPS-NA, NA-FORMATE, PEG 4000, REMARK 280 ETHYLENEGLYCOL, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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 63.52500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 63.52500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.38500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11940 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 613 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 106 REMARK 465 SER A 107 REMARK 465 HIS A 108 REMARK 465 MET A 109 REMARK 465 GLY A 110 REMARK 465 SER A 111 REMARK 465 PRO A 112 REMARK 465 ASN A 113 REMARK 465 SER A 114 REMARK 465 PRO A 115 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 207 REMARK 465 GLY A 208 REMARK 465 SER A 209 REMARK 465 THR A 210 REMARK 465 GLY A 211 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 ASN A 420 REMARK 465 GLU A 421 REMARK 465 ILE A 422 REMARK 465 SER A 423 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 ARG A 248 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 405 CG CD OE1 OE2 REMARK 470 LYS C 625 CG CD CE NZ 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 278 -73.23 -56.76 REMARK 500 TYR A 289 44.11 -108.92 REMARK 500 ASP A 344 75.05 -101.00 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 YA1 A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WT5 RELATED DB: PDB REMARK 900 RELATED ID: 3WT7 RELATED DB: PDB DBREF 3WT6 A 116 423 UNP P13053 VDR_RAT 116 423 DBREF 3WT6 C 625 637 UNP Q15648 MED1_HUMAN 640 652 SEQADV 3WT6 GLY A 106 UNP P13053 EXPRESSION TAG SEQADV 3WT6 SER A 107 UNP P13053 EXPRESSION TAG SEQADV 3WT6 HIS A 108 UNP P13053 EXPRESSION TAG SEQADV 3WT6 MET A 109 UNP P13053 EXPRESSION TAG SEQADV 3WT6 GLY A 110 UNP P13053 EXPRESSION TAG SEQADV 3WT6 SER A 111 UNP P13053 EXPRESSION TAG SEQADV 3WT6 PRO A 112 UNP P13053 EXPRESSION TAG SEQADV 3WT6 ASN A 113 UNP P13053 EXPRESSION TAG SEQADV 3WT6 SER A 114 UNP P13053 EXPRESSION TAG SEQADV 3WT6 PRO A 115 UNP P13053 EXPRESSION TAG SEQADV 3WT6 A UNP P13053 SER 165 DELETION SEQADV 3WT6 A UNP P13053 TYR 166 DELETION SEQADV 3WT6 A UNP P13053 SER 167 DELETION SEQADV 3WT6 A UNP P13053 PRO 168 DELETION SEQADV 3WT6 A UNP P13053 ARG 169 DELETION SEQADV 3WT6 A UNP P13053 PRO 170 DELETION SEQADV 3WT6 A UNP P13053 THR 171 DELETION SEQADV 3WT6 A UNP P13053 LEU 172 DELETION SEQADV 3WT6 A UNP P13053 SER 173 DELETION SEQADV 3WT6 A UNP P13053 PHE 174 DELETION SEQADV 3WT6 A UNP P13053 SER 175 DELETION SEQADV 3WT6 A UNP P13053 GLY 176 DELETION SEQADV 3WT6 A UNP P13053 ASN 177 DELETION SEQADV 3WT6 A UNP P13053 SER 178 DELETION SEQADV 3WT6 A UNP P13053 SER 179 DELETION SEQADV 3WT6 A UNP P13053 SER 180 DELETION SEQADV 3WT6 A UNP P13053 SER 181 DELETION SEQADV 3WT6 A UNP P13053 SER 182 DELETION SEQADV 3WT6 A UNP P13053 SER 183 DELETION SEQADV 3WT6 A UNP P13053 ASP 184 DELETION SEQADV 3WT6 A UNP P13053 LEU 185 DELETION SEQADV 3WT6 A UNP P13053 TYR 186 DELETION SEQADV 3WT6 A UNP P13053 THR 187 DELETION SEQADV 3WT6 A UNP P13053 THR 188 DELETION SEQADV 3WT6 A UNP P13053 SER 189 DELETION SEQADV 3WT6 A UNP P13053 LEU 190 DELETION SEQADV 3WT6 A UNP P13053 ASP 191 DELETION SEQADV 3WT6 A UNP P13053 MET 192 DELETION SEQADV 3WT6 A UNP P13053 MET 193 DELETION SEQADV 3WT6 A UNP P13053 GLU 194 DELETION SEQADV 3WT6 A UNP P13053 PRO 195 DELETION SEQADV 3WT6 A UNP P13053 SER 196 DELETION SEQADV 3WT6 A UNP P13053 GLY 197 DELETION SEQADV 3WT6 A UNP P13053 PHE 198 DELETION SEQADV 3WT6 A UNP P13053 SER 199 DELETION SEQADV 3WT6 A UNP P13053 ASN 200 DELETION SEQADV 3WT6 A UNP P13053 LEU 201 DELETION SEQADV 3WT6 A UNP P13053 ASP 202 DELETION SEQADV 3WT6 A UNP P13053 LEU 203 DELETION SEQADV 3WT6 A UNP P13053 ASN 204 DELETION SEQADV 3WT6 A UNP P13053 GLY 205 DELETION SEQADV 3WT6 A UNP P13053 GLU 206 DELETION SEQADV 3WT6 A UNP P13053 ASP 207 DELETION SEQADV 3WT6 A UNP P13053 SER 208 DELETION SEQADV 3WT6 A UNP P13053 ASP 209 DELETION SEQADV 3WT6 A UNP P13053 ASP 210 DELETION SEQADV 3WT6 A UNP P13053 PRO 211 DELETION SEQRES 1 A 271 GLY SER HIS MET GLY SER PRO ASN SER PRO LEU LYS ASP SEQRES 2 A 271 SER LEU ARG PRO LYS LEU SER GLU GLU GLN GLN HIS ILE SEQRES 3 A 271 ILE ALA ILE LEU LEU ASP ALA HIS HIS LYS THR TYR ASP SEQRES 4 A 271 PRO THR TYR ALA ASP PHE ARG ASP PHE ARG PRO PRO VAL SEQRES 5 A 271 ARG MET ASP GLY SER THR GLY SER VAL THR LEU ASP LEU SEQRES 6 A 271 SER PRO LEU SER MET LEU PRO HIS LEU ALA ASP LEU VAL SEQRES 7 A 271 SER TYR SER ILE GLN LYS VAL ILE GLY PHE ALA LYS MET SEQRES 8 A 271 ILE PRO GLY PHE ARG ASP LEU THR SER ASP ASP GLN ILE SEQRES 9 A 271 VAL LEU LEU LYS SER SER ALA ILE GLU VAL ILE MET LEU SEQRES 10 A 271 ARG SER ASN GLN SER PHE THR MET ASP ASP MET SER TRP SEQRES 11 A 271 ASP CYS GLY SER GLN ASP TYR LYS TYR ASP VAL THR ASP SEQRES 12 A 271 VAL SER LYS ALA GLY HIS THR LEU GLU LEU ILE GLU PRO SEQRES 13 A 271 LEU ILE LYS PHE GLN VAL GLY LEU LYS LYS LEU ASN LEU SEQRES 14 A 271 HIS GLU GLU GLU HIS VAL LEU LEU MET ALA ILE CYS ILE SEQRES 15 A 271 VAL SER PRO ASP ARG PRO GLY VAL GLN ASP ALA LYS LEU SEQRES 16 A 271 VAL GLU ALA ILE GLN ASP ARG LEU SER ASN THR LEU GLN SEQRES 17 A 271 THR TYR ILE ARG CYS ARG HIS PRO PRO PRO GLY SER HIS SEQRES 18 A 271 GLN LEU TYR ALA LYS MET ILE GLN LYS LEU ALA ASP LEU SEQRES 19 A 271 ARG SER LEU ASN GLU GLU HIS SER LYS GLN TYR ARG SER SEQRES 20 A 271 LEU SER PHE GLN PRO GLU ASN SER MET LYS LEU THR PRO SEQRES 21 A 271 LEU VAL LEU GLU VAL PHE GLY ASN GLU ILE SER SEQRES 1 C 13 LYS ASN HIS PRO MET LEU MET ASN LEU LEU LYS ASP ASN HET YA1 A 501 68 HETNAM YA1 (1R,3R,7E,17BETA)-17-[(2R,3R)-3-BUTYL-6-HYDROXY-6- HETNAM 2 YA1 METHYLHEPTAN-2-YL]-2-METHYLIDENE-9,10-SECOESTRA-5,7- HETNAM 3 YA1 DIENE-1,3-DIOL FORMUL 3 YA1 C31 H52 O3 FORMUL 4 HOH *58(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 LEU A 319 1 18 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 PRO A 370 GLN A 403 1 34 HELIX 11 11 GLN A 403 MET A 408 1 6 HELIX 12 12 THR A 411 PHE A 418 1 8 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 3.17 SITE 1 AC1 19 TYR A 143 LEU A 223 VAL A 230 SER A 233 SITE 2 AC1 19 ILE A 264 MET A 268 ARG A 270 SER A 271 SITE 3 AC1 19 SER A 274 TRP A 282 CYS A 284 ALA A 299 SITE 4 AC1 19 HIS A 301 LEU A 305 LEU A 309 HIS A 393 SITE 5 AC1 19 PHE A 418 HOH A 601 HOH A 655 CRYST1 127.050 44.770 45.110 90.00 94.20 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 0.007871 0.000000 0.000578 0.00000 SCALE2 0.000000 0.022336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022228 0.00000