HEADER TRANSCRIPTION 04-JUL-15 5AWJ TITLE CRYSTAL STRUCTURE OF VDR-LBD/PARTIAL AGONIST COMPLEX: 22S-HEXYL TITLE 2 ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR,VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 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,VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR, COMPND 7 NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: DELETION MUTANT, RESIDUES 165-211; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: MEDIATOR OF RNA POLYMERASE II TRANSCRIPTION SUBUNIT 1; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: UNP RESIDUES 640-652; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS TRANSCRIPTION, VITAMIN D3, VDRE, RXR, CO-FACTORS EXPDTA X-RAY DIFFRACTION AUTHOR Y.ANAMI,T.ITOH,Y.INABA,M.NAKABAYASHI,T.IKURA,N.ITO,K.YAMAMOTO REVDAT 3 20-MAR-24 5AWJ 1 REMARK REVDAT 2 26-FEB-20 5AWJ 1 JRNL REMARK REVDAT 1 18-NOV-15 5AWJ 0 JRNL AUTH Y.ANAMI,Y.SAKAMAKI,T.ITOH,Y.INABA,M.NAKABAYASHI,T.IKURA, JRNL AUTH 2 N.ITO,K.YAMAMOTO JRNL TITL FINE TUNING OF AGONISTIC/ANTAGONISTIC ACTIVITY FOR VITAMIN D JRNL TITL 2 RECEPTOR BY 22-ALKYL CHAIN LENGTH OF LIGANDS: 22S-HEXYL JRNL TITL 3 COMPOUND UNEXPECTEDLY RESTORED AGONISTIC ACTIVITY. JRNL REF BIOORG.MED.CHEM. V. 23 7274 2015 JRNL REFN ESSN 1464-3391 JRNL PMID 26515040 JRNL DOI 10.1016/J.BMC.2015.10.026 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 13166 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) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 694 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 826 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 43 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2005 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.50000 REMARK 3 B22 (A**2) : 3.65000 REMARK 3 B33 (A**2) : 0.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.70000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.331 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.237 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.205 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.037 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2166 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2159 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2935 ; 1.672 ; 2.032 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4999 ; 3.366 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 252 ; 4.761 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 92 ;37.533 ;24.565 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 386 ;20.086 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;19.592 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 338 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2314 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 463 ; 0.027 ; 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): 1005 ; 4.083 ; 7.251 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1004 ; 4.075 ; 7.250 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1252 ; 6.197 ;10.850 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1253 ; 6.195 ;10.851 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1161 ; 4.567 ; 7.656 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1162 ; 4.565 ; 7.654 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1682 ; 7.225 ;11.301 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2450 ; 9.316 ;57.511 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2451 ; 9.314 ;57.512 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 420 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1784 -21.9492 -18.9908 REMARK 3 T TENSOR REMARK 3 T11: 0.0725 T22: 0.0726 REMARK 3 T33: 0.0885 T12: 0.0115 REMARK 3 T13: 0.0199 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 0.7096 L22: 0.0061 REMARK 3 L33: 0.1210 L12: 0.0028 REMARK 3 L13: -0.2387 L23: 0.0120 REMARK 3 S TENSOR REMARK 3 S11: -0.0625 S12: -0.0260 S13: 0.0388 REMARK 3 S21: 0.0004 S22: 0.0139 S23: 0.0213 REMARK 3 S31: 0.0523 S32: 0.0235 S33: 0.0487 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): 11.7148 -10.8374 -11.3892 REMARK 3 T TENSOR REMARK 3 T11: 0.0802 T22: 0.1191 REMARK 3 T33: 0.0798 T12: -0.0078 REMARK 3 T13: 0.0011 T23: -0.0631 REMARK 3 L TENSOR REMARK 3 L11: 3.7355 L22: 1.0492 REMARK 3 L33: 5.0183 L12: -1.2236 REMARK 3 L13: 1.4319 L23: -2.1694 REMARK 3 S TENSOR REMARK 3 S11: 0.0287 S12: -0.0327 S13: 0.1427 REMARK 3 S21: 0.1502 S22: -0.0414 S23: -0.0297 REMARK 3 S31: -0.4103 S32: 0.0483 S33: 0.0127 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 601 A 634 REMARK 3 RESIDUE RANGE : C 701 C 701 REMARK 3 ORIGIN FOR THE GROUP (A): 25.1691 -22.6002 -17.0173 REMARK 3 T TENSOR REMARK 3 T11: 0.0716 T22: 0.0521 REMARK 3 T33: 0.0987 T12: 0.0051 REMARK 3 T13: 0.0362 T23: 0.0156 REMARK 3 L TENSOR REMARK 3 L11: 0.3481 L22: 0.1903 REMARK 3 L33: 0.1016 L12: -0.1510 REMARK 3 L13: -0.0318 L23: 0.1108 REMARK 3 S TENSOR REMARK 3 S11: -0.0285 S12: -0.0762 S13: 0.0670 REMARK 3 S21: 0.0060 S22: -0.0076 S23: -0.0196 REMARK 3 S31: 0.0360 S32: -0.0209 S33: 0.0361 REMARK 3 REMARK 3 TLS GROUP : 4 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): 19.6389 -25.7429 -25.3050 REMARK 3 T TENSOR REMARK 3 T11: 0.1453 T22: 0.1098 REMARK 3 T33: 0.0494 T12: 0.0006 REMARK 3 T13: 0.0260 T23: -0.0083 REMARK 3 L TENSOR REMARK 3 L11: 2.0320 L22: 1.7607 REMARK 3 L33: 2.1746 L12: -1.8851 REMARK 3 L13: -2.0967 L23: 1.9565 REMARK 3 S TENSOR REMARK 3 S11: 0.1294 S12: 0.3832 S13: -0.1736 REMARK 3 S21: -0.0633 S22: -0.3408 S23: 0.1739 REMARK 3 S31: -0.0778 S32: -0.3951 S33: 0.2114 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 5AWJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1300000089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14125 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.3000 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOPS-NA, NA-FORMATE, PEG 4000, REMARK 280 ETHYLENEGLYCOL, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 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 76.73850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.72350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 76.73850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.72350 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: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 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 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 151 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 311 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O VAL A 157 OG SER A 221 2.03 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 124 78.15 -67.86 REMARK 500 ASP A 279 26.38 -145.20 REMARK 500 CYS A 284 61.26 -105.53 REMARK 500 GLN A 343 -73.30 -86.68 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 YSL A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AWK RELATED DB: PDB DBREF 5AWJ A 116 211 UNP P13053 VDR_RAT 116 164 DBREF 5AWJ A 212 423 UNP P13053 VDR_RAT 212 423 DBREF 5AWJ C 625 637 UNP Q15648 MED1_HUMAN 640 652 SEQADV 5AWJ GLY A 106 UNP P13053 EXPRESSION TAG SEQADV 5AWJ SER A 107 UNP P13053 EXPRESSION TAG SEQADV 5AWJ HIS A 108 UNP P13053 EXPRESSION TAG SEQADV 5AWJ MET A 109 UNP P13053 EXPRESSION TAG SEQADV 5AWJ GLY A 110 UNP P13053 EXPRESSION TAG SEQADV 5AWJ SER A 111 UNP P13053 EXPRESSION TAG SEQADV 5AWJ PRO A 112 UNP P13053 EXPRESSION TAG SEQADV 5AWJ ASN A 113 UNP P13053 EXPRESSION TAG SEQADV 5AWJ SER A 114 UNP P13053 EXPRESSION TAG SEQADV 5AWJ PRO A 115 UNP P13053 EXPRESSION TAG 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 YSL A 501 99 HETNAM YSL (1R,3R)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-(2- HETNAM 2 YSL HYDROXYETHYL)NONAN-2-YL]-7A-METHYL-2,3,3A,5,6,7- HETNAM 3 YSL HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-2- HETNAM 4 YSL METHYLIDENE-CYCLOHEXANE-1,3-DIOL FORMUL 3 YSL C30 H50 O3 FORMUL 4 HOH *35(H2 O) HELIX 1 AA1 SER A 125 TYR A 143 1 19 HELIX 2 AA2 TYR A 147 PHE A 153 5 7 HELIX 3 AA3 MET A 222 MET A 243 1 22 HELIX 4 AA4 GLY A 246 LEU A 250 5 5 HELIX 5 AA5 THR A 251 ASN A 272 1 22 HELIX 6 AA6 SER A 286 ASP A 288 5 3 HELIX 7 AA7 ASP A 292 LYS A 298 1 7 HELIX 8 AA8 THR A 302 LEU A 319 1 18 HELIX 9 AA9 HIS A 322 VAL A 335 1 14 HELIX 10 AB1 ASP A 344 HIS A 367 1 24 HELIX 11 AB2 GLN A 374 GLN A 403 1 30 HELIX 12 AB3 GLN A 403 MET A 408 1 6 HELIX 13 AB4 THR A 411 GLY A 419 1 9 HELIX 14 AB5 HIS C 627 LYS C 635 1 9 SHEET 1 AA1 3 PHE A 275 THR A 276 0 SHEET 2 AA1 3 SER A 281 ASP A 283 -1 O SER A 281 N THR A 276 SHEET 3 AA1 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 -2.89 CISPEP 2 LYS C 625 ASN C 626 0 -0.52 SITE 1 AC1 15 TYR A 143 LEU A 223 VAL A 230 SER A 233 SITE 2 AC1 15 ARG A 270 SER A 271 SER A 274 TRP A 282 SITE 3 AC1 15 CYS A 284 VAL A 296 HIS A 301 LEU A 305 SITE 4 AC1 15 LEU A 389 HIS A 393 PHE A 418 CRYST1 153.477 43.447 42.317 90.00 100.53 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 0.006516 0.000000 0.001212 0.00000 SCALE2 0.000000 0.023017 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024036 0.00000