HEADER TRANSCRIPTION 04-JUL-15 5AWK TITLE CRYSTAL STRUCTURE OF VDR-LBD/PARTIAL AGONIST COMPLEX: 22S-ETHYL 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 TRANDCRIPTION, VITAMIN D, VDRE, RXR, CO-FACTORS, HORMONE, KEYWDS 2 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR Y.ANAMI,T.ITOH,K.YAMAMOTO REVDAT 2 26-FEB-20 5AWK 1 JRNL REMARK REVDAT 1 18-NOV-15 5AWK 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. 2.90 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 74.2 REMARK 3 NUMBER OF REFLECTIONS : 4318 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 207 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 341 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 77.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 19 REMARK 3 BIN FREE R VALUE : 0.4840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2004 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.08000 REMARK 3 B22 (A**2) : 6.24000 REMARK 3 B33 (A**2) : 0.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.28000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.596 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.389 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 49.299 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2076 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2034 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2810 ; 1.128 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4697 ; 3.471 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 248 ; 3.937 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 91 ;25.795 ;24.505 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 378 ;16.584 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;11.484 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 322 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2268 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 449 ; 0.021 ; 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): 1001 ; 2.715 ; 6.449 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1000 ; 2.715 ; 6.447 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1246 ; 4.610 ; 9.646 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1247 ; 4.608 ; 9.648 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1075 ; 2.769 ; 6.660 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1076 ; 2.768 ; 6.658 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1565 ; 4.686 ; 9.860 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2511 ; 7.314 ;50.991 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2512 ; 7.312 ;50.987 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): 19.0792 0.3727 19.1431 REMARK 3 T TENSOR REMARK 3 T11: 0.2531 T22: 0.2832 REMARK 3 T33: 0.2763 T12: -0.0144 REMARK 3 T13: -0.0008 T23: -0.0134 REMARK 3 L TENSOR REMARK 3 L11: 0.7109 L22: 0.0655 REMARK 3 L33: 0.0736 L12: -0.1344 REMARK 3 L13: 0.0070 L23: -0.0511 REMARK 3 S TENSOR REMARK 3 S11: -0.0001 S12: -0.0261 S13: -0.0138 REMARK 3 S21: -0.0164 S22: -0.0083 S23: 0.0142 REMARK 3 S31: -0.0280 S32: 0.0118 S33: 0.0084 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): 5.9204 -11.0946 11.0565 REMARK 3 T TENSOR REMARK 3 T11: 0.2403 T22: 0.2882 REMARK 3 T33: 0.3030 T12: 0.0139 REMARK 3 T13: 0.0091 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 2.9373 L22: 0.8313 REMARK 3 L33: 1.4871 L12: 1.4336 REMARK 3 L13: -0.5122 L23: -0.6706 REMARK 3 S TENSOR REMARK 3 S11: 0.1053 S12: 0.0691 S13: -0.0776 REMARK 3 S21: 0.0500 S22: -0.0198 S23: 0.0267 REMARK 3 S31: 0.0369 S32: 0.1274 S33: -0.0856 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): 13.3559 4.6223 24.7574 REMARK 3 T TENSOR REMARK 3 T11: 0.2791 T22: 0.2671 REMARK 3 T33: 0.3221 T12: 0.0165 REMARK 3 T13: 0.0218 T23: -0.0058 REMARK 3 L TENSOR REMARK 3 L11: 3.7934 L22: 8.9951 REMARK 3 L33: 11.6579 L12: 3.4191 REMARK 3 L13: 1.4496 L23: -6.7960 REMARK 3 S TENSOR REMARK 3 S11: 0.1342 S12: -0.0839 S13: -0.1951 REMARK 3 S21: 0.1400 S22: -0.2326 S23: -0.2508 REMARK 3 S31: -0.0615 S32: 0.2531 S33: 0.0984 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 601 A 608 REMARK 3 ORIGIN FOR THE GROUP (A): 20.3945 3.5032 19.1831 REMARK 3 T TENSOR REMARK 3 T11: 0.2197 T22: 0.0980 REMARK 3 T33: 0.3550 T12: -0.0529 REMARK 3 T13: 0.0406 T23: 0.0636 REMARK 3 L TENSOR REMARK 3 L11: 0.1991 L22: 0.6389 REMARK 3 L33: 2.1816 L12: -0.3006 REMARK 3 L13: -0.5382 L23: 1.1779 REMARK 3 S TENSOR REMARK 3 S11: 0.0114 S12: 0.0913 S13: 0.1041 REMARK 3 S21: 0.0082 S22: -0.0364 S23: -0.0113 REMARK 3 S31: 0.0484 S32: -0.0896 S33: 0.0250 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 5AWK 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_1300000090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-14 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 : 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : IMOSFLM REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9246 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.2 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 56.0000 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 (%): 41.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 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 77.01500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.98500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 77.01500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.98500 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: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11750 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 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 ASP A 279 CG OD1 OD2 REMARK 470 LYS A 346 CG CD CE NZ REMARK 470 LYS A 395 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 ALA A 138 OG1 THR A 142 1.85 REMARK 500 O LEU A 136 ND1 HIS A 140 2.10 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 HIS C 627 77.22 -108.48 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 YSE A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AWJ RELATED DB: PDB DBREF 5AWK A 116 211 UNP P13053 VDR_RAT 116 164 DBREF 5AWK A 212 423 UNP P13053 VDR_RAT 212 423 DBREF 5AWK C 625 637 UNP Q15648 MED1_HUMAN 640 652 SEQADV 5AWK GLY A 106 UNP P13053 EXPRESSION TAG SEQADV 5AWK SER A 107 UNP P13053 EXPRESSION TAG SEQADV 5AWK HIS A 108 UNP P13053 EXPRESSION TAG SEQADV 5AWK MET A 109 UNP P13053 EXPRESSION TAG SEQADV 5AWK GLY A 110 UNP P13053 EXPRESSION TAG SEQADV 5AWK SER A 111 UNP P13053 EXPRESSION TAG SEQADV 5AWK PRO A 112 UNP P13053 EXPRESSION TAG SEQADV 5AWK ASN A 113 UNP P13053 EXPRESSION TAG SEQADV 5AWK SER A 114 UNP P13053 EXPRESSION TAG SEQADV 5AWK 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 YSE A 501 29 HETNAM YSE (1R,3R)-5-[(2E)-2-[(1R,3AS,7AR)-1-[(2R,3S)-3-ETHYL-5- HETNAM 2 YSE OXIDANYL-PENTAN-2-YL]-7A-METHYL-2,3,3A,5,6,7- HETNAM 3 YSE HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-2- HETNAM 4 YSE METHYLIDENE-CYCLOHEXANE-1,3-DIOL FORMUL 3 YSE C26 H42 O3 FORMUL 4 HOH *8(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 ILE A 244 1 23 HELIX 4 AA4 THR A 251 SER A 271 1 21 HELIX 5 AA5 ASP A 292 HIS A 301 1 10 HELIX 6 AA6 THR A 302 ASN A 320 1 19 HELIX 7 AA7 HIS A 322 VAL A 335 1 14 HELIX 8 AA8 ASP A 344 HIS A 367 1 24 HELIX 9 AA9 GLN A 374 GLN A 403 1 30 HELIX 10 AB1 GLN A 403 MET A 408 1 6 HELIX 11 AB2 THR A 411 GLY A 419 1 9 HELIX 12 AB3 HIS C 627 LYS C 635 1 9 SHEET 1 AA1 2 PHE A 275 THR A 276 0 SHEET 2 AA1 2 SER A 281 TRP A 282 -1 O SER A 281 N THR A 276 CISPEP 1 PRO A 369 PRO A 370 0 -0.55 SITE 1 AC1 11 TYR A 143 LEU A 229 SER A 233 ARG A 270 SITE 2 AC1 11 SER A 271 SER A 274 TRP A 282 VAL A 296 SITE 3 AC1 11 HIS A 301 LEU A 305 HIS A 393 CRYST1 154.030 41.970 41.860 90.00 95.96 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 0.006492 0.000000 0.000678 0.00000 SCALE2 0.000000 0.023827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024019 0.00000 MASTER 398 0 1 12 2 0 3 6 0 0 0 22 END