PDB Short entry for 3X36 HEADER TRANSCRIPTION 16-JAN-15 3X36 TITLE CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND BINDING TITLE 2 DOMAIN COMPLEXED WITH 7,8-CIS-1A,25-DIHYDROXY-19-NORVITAMIN D3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LIGAND BINDING DOMAIN (UNP RESIDUES 118-164, 216-427); 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 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NR1I1, VDR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION, HORMONE RECEPTOR EXPDTA X-RAY DIFFRACTION AUTHOR M.TAKIMOTO-KAMIMURA,S.KAKUDA REVDAT 3 20-MAR-24 3X36 1 REMARK SEQADV REVDAT 2 23-AUG-17 3X36 1 SOURCE REMARK REVDAT 1 20-JAN-16 3X36 0 JRNL AUTH D.SAWADA,H.SAITO,S.KAKUDA,M.TAKIMOTO-KAMIMURA,Y.MATSUMOTO, JRNL AUTH 2 K.TAKAGI,E.OCHIAI,A.KITTAKA JRNL TITL REVISITING THE 7,8-CIS-VITAMIN D3 DERIVATIVES: SYNTHESIS, JRNL TITL 2 EVALUATING THE BIOLOGICAL ACTIVITY, AND STUDY OF THE BINDING JRNL TITL 3 CONFIGURATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.93 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 78.0 REMARK 3 NUMBER OF REFLECTIONS : 17506 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 939 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 291 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 17.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 13 REMARK 3 BIN FREE R VALUE : 0.2180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2022 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 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) : 18.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.55000 REMARK 3 B22 (A**2) : -0.38000 REMARK 3 B33 (A**2) : 0.93000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.196 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.095 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.210 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2193 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2150 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2981 ; 2.116 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4981 ; 1.004 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 6.946 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 98 ;37.625 ;24.184 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 410 ;17.272 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.651 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 337 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2449 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 480 ; 0.002 ; 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 : NULL 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 3X36 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000097120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95370 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 47.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 24.8 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 <I/SIGMA(I)> 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, PH6.5, 1.2-1.6M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 22.40950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.08300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.63500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.08300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.40950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.63500 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 114 REMARK 465 SER A 115 REMARK 465 HIS A 116 REMARK 465 MET A 117 REMARK 465 GLY A 164 REMARK 465 ASN A 424 REMARK 465 GLU A 425 REMARK 465 ILE A 426 REMARK 465 SER A 427 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 HOH A 691 O HOH A 718 1.37 REMARK 500 O HOH A 692 O HOH A 719 1.58 REMARK 500 O LEU A 219 CB GLU A 220 1.70 REMARK 500 NZ LYS A 315 O HOH A 670 1.73 REMARK 500 OD2 ASP A 161 OE1 GLU A 220 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 693 O HOH A 717 4445 1.47 REMARK 500 O HOH A 668 O HOH A 676 3654 1.95 REMARK 500 NE ARG A 402 O HOH A 661 3554 1.97 REMARK 500 O HOH A 670 O HOH A 678 3654 2.07 REMARK 500 O HOH A 656 O HOH A 672 3644 2.10 REMARK 500 O HOH A 669 O HOH A 677 3654 2.10 REMARK 500 REMARK 500 REMARK: NULL 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 GLU A 220 C - N - CA ANGL. DEV. = -16.9 DEGREES REMARK 500 LEU A 390 CB - CG - CD1 ANGL. DEV. = 12.0 DEGREES REMARK 500 MET A 412 CB - CG - SD ANGL. DEV. = 21.3 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 SER A 119 111.38 -14.94 REMARK 500 GLU A 220 -61.20 111.45 REMARK 500 ASP A 283 18.27 -146.29 REMARK 500 GLN A 291 -56.36 56.33 REMARK 500 GLN A 347 -71.89 -95.33 REMARK 500 ASP A 348 74.90 -100.32 REMARK 500 SER A 376 33.74 -82.36 REMARK 500 SER A 376 31.63 -82.36 REMARK 500 LEU A 414 -156.69 -97.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 289 ASN A 290 41.47 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 41W A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X31 RELATED DB: PDB DBREF 3X36 A 118 164 UNP P11473 VDR_HUMAN 118 164 DBREF 3X36 A 216 427 UNP P11473 VDR_HUMAN 216 427 SEQADV 3X36 GLY A 114 UNP P11473 EXPRESSION TAG SEQADV 3X36 SER A 115 UNP P11473 EXPRESSION TAG SEQADV 3X36 HIS A 116 UNP P11473 EXPRESSION TAG SEQADV 3X36 MET A 117 UNP P11473 EXPRESSION TAG SEQRES 1 A 263 GLY SER HIS MET ASP SER LEU ARG PRO LYS LEU SER GLU SEQRES 2 A 263 GLU GLN GLN ARG ILE ILE ALA ILE LEU LEU ASP ALA HIS SEQRES 3 A 263 HIS LYS THR TYR ASP PRO THR TYR SER ASP PHE CYS GLN SEQRES 4 A 263 PHE ARG PRO PRO VAL ARG VAL ASN ASP GLY GLY GLY SER SEQRES 5 A 263 VAL THR LEU GLU LEU SER GLN LEU SER MET LEU PRO HIS SEQRES 6 A 263 LEU ALA ASP LEU VAL SER TYR SER ILE GLN LYS VAL ILE SEQRES 7 A 263 GLY PHE ALA LYS MET ILE PRO GLY PHE ARG ASP LEU THR SEQRES 8 A 263 SER GLU ASP GLN ILE VAL LEU LEU LYS SER SER ALA ILE SEQRES 9 A 263 GLU VAL ILE MET LEU ARG SER ASN GLU SER PHE THR MET SEQRES 10 A 263 ASP ASP MET SER TRP THR CYS GLY ASN GLN ASP TYR LYS SEQRES 11 A 263 TYR ARG VAL SER ASP VAL THR LYS ALA GLY HIS SER LEU SEQRES 12 A 263 GLU LEU ILE GLU PRO LEU ILE LYS PHE GLN VAL GLY LEU SEQRES 13 A 263 LYS LYS LEU ASN LEU HIS GLU GLU GLU HIS VAL LEU LEU SEQRES 14 A 263 MET ALA ILE CYS ILE VAL SER PRO ASP ARG PRO GLY VAL SEQRES 15 A 263 GLN ASP ALA ALA LEU ILE GLU ALA ILE GLN ASP ARG LEU SEQRES 16 A 263 SER ASN THR LEU GLN THR TYR ILE ARG CYS ARG HIS PRO SEQRES 17 A 263 PRO PRO GLY SER HIS LEU LEU TYR ALA LYS MET ILE GLN SEQRES 18 A 263 LYS LEU ALA ASP LEU ARG SER LEU ASN GLU GLU HIS SER SEQRES 19 A 263 LYS GLN TYR ARG CYS LEU SER PHE GLN PRO GLU CYS SER SEQRES 20 A 263 MET LYS LEU THR PRO LEU VAL LEU GLU VAL PHE GLY ASN SEQRES 21 A 263 GLU ILE SER HET 41W A 501 29 HETNAM 41W (1R,3R)-5-[(2Z)-2-[(1R,3AS,7AR)-7A-METHYL-1-[(2R)-6- HETNAM 2 41W METHYL-6-OXIDANYL-HEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO- HETNAM 3 41W 1H-INDEN-4-YLIDENE]ETHYLIDENE]CYCLOHEXANE-1,3-DIOL FORMUL 2 41W C26 H44 O3 FORMUL 3 HOH *131(H2 O) HELIX 1 1 SER A 125 TYR A 143 1 19 HELIX 2 2 ASP A 149 PHE A 153 5 5 HELIX 3 3 VAL A 217 SER A 222 1 6 HELIX 4 4 MET A 226 MET A 247 1 22 HELIX 5 5 GLY A 250 LEU A 254 5 5 HELIX 6 6 THR A 255 SER A 275 1 21 HELIX 7 7 ARG A 296 LYS A 302 1 7 HELIX 8 8 SER A 306 LEU A 323 1 18 HELIX 9 9 HIS A 326 VAL A 339 1 14 HELIX 10 10 ASP A 348 HIS A 371 1 24 HELIX 11 11 GLY A 375 HIS A 377 5 3 HELIX 12 12 LEU A 378 SER A 405 1 28 HELIX 13 13 GLU A 409 LEU A 414 1 6 HELIX 14 14 THR A 415 GLY A 423 1 9 SHEET 1 A 3 PHE A 279 THR A 280 0 SHEET 2 A 3 SER A 285 THR A 287 -1 O SER A 285 N THR A 280 SHEET 3 A 3 LYS A 294 TYR A 295 -1 O TYR A 295 N TRP A 286 CISPEP 1 PRO A 372 PRO A 373 0 -14.54 CISPEP 2 PRO A 373 PRO A 374 0 2.40 SITE 1 AC1 10 TYR A 143 LEU A 227 SER A 237 ARG A 274 SITE 2 AC1 10 SER A 275 SER A 278 TRP A 286 VAL A 300 SITE 3 AC1 10 HIS A 305 HIS A 397 CRYST1 44.819 51.270 132.166 90.00 90.00 90.00 P 21 21 21 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 0.022312 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019505 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007566 0.00000