HEADER TRANSCRIPTION 18-AUG-16 5GT4 TITLE CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND BINDING TITLE 2 DOMAIN COMPLEXED WITH (1R,2S,3R,5Z,7E,14BETA,17ALPHA)-2-CYANOPROPOXY- TITLE 3 9,10-SECOCHOLESTA-5,7,10-TRIENE-1,3,25-TRIOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: VITAMIN D3 RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 118-164,216-423; COMPND 5 SYNONYM: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR COMPND 6 SUBFAMILY 1 GROUP I MEMBER 1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: VDR, NR1I1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NUCLEAR HORMONE RECEPTOR FULL AGONIST LIGAND COMPLEX, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR M.TAKIMOTO-KAMIMURA REVDAT 3 08-NOV-23 5GT4 1 REMARK REVDAT 2 26-FEB-20 5GT4 1 REMARK REVDAT 1 09-NOV-16 5GT4 0 SPRSDE 09-NOV-16 5GT4 4PA2 JRNL AUTH M.TAKIMOTO-KAMIMURA JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND JRNL TITL 2 BINDING DOMAIN COMPLEXED WITH JRNL TITL 3 (1R,2S,3R,5Z,7E,14BETA,17ALPHA)-2-CYANOPROPOXY-9, JRNL TITL 4 10-SECOCHOLESTA-5,7,10-TRIENE-1,3,25-TRIOL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.83 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 26427 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1394 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) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1883 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.2950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2027 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 71 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.82000 REMARK 3 B22 (A**2) : -0.53000 REMARK 3 B33 (A**2) : 1.35000 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): 0.124 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.414 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2145 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2093 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2909 ; 2.244 ; 2.005 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4842 ; 1.057 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 261 ; 7.288 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;36.358 ;24.255 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 393 ;15.675 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;18.969 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 332 ; 0.147 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2372 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 464 ; 0.007 ; 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 : NULL 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: THE AUTHORS STATE THEY REMOVED THE LONG REMARK 3 LOOP 165-215 FOR THE CRYSTALLIZATION WITH DIRECT LINCAGE WITH REMARK 3 GLY 164 AND SER 216, SO THIS REGION RECIEVED QUITE LARGE STERIC REMARK 3 HINDRANCE AND RESULED ABNORMAL BOND LENGTH AS USUAL, AND THAT REMARK 3 THE BOND IS EXISTING IN REAL BUT THE BOND DISTANCE IS ABNORMAL REMARK 3 BY THE DISORDER BY THE STERIC HINDRANCES. REMARK 4 REMARK 4 5GT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1300001398. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-14 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 : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27881 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.827 REMARK 200 RESOLUTION RANGE LOW (A) : 65.738 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 FOR THE DATA SET : 13.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.47000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 11.0.05 REMARK 200 STARTING MODEL: 1DB1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES, 1.4M AMMONIUM SULPHATE, PH REMARK 280 6.5, EVAPORATION, TEMPERATURE 277K 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 22.33150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.73750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.92100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.73750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.33150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.92100 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 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 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 GLY A 164 N SER A 216 1.66 REMARK 500 OH TYR A 147 O HOH A 601 1.78 REMARK 500 O HOH A 656 O HOH A 666 1.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 277 CG GLU A 277 CD 0.104 REMARK 500 CYS A 369 CB CYS A 369 SG -0.141 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 ASP A 144 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 TYR A 147 CB - CG - CD1 ANGL. DEV. = 3.8 DEGREES REMARK 500 CYS A 369 CB - CA - C ANGL. DEV. = -20.0 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 74.05 26.09 REMARK 500 ASP A 161 44.15 -154.01 REMARK 500 LEU A 224 48.19 39.96 REMARK 500 ASP A 283 17.59 -150.95 REMARK 500 CYS A 288 56.59 -106.41 REMARK 500 ASN A 290 153.98 172.47 REMARK 500 SER A 376 51.41 -66.56 REMARK 500 HIS A 377 23.52 -74.08 REMARK 500 LEU A 414 -152.87 -94.98 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 163 GLY A 164 -58.29 REMARK 500 PRO A 374 GLY A 375 148.27 REMARK 500 SER A 376 HIS A 377 146.16 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 2KB A 501 DBREF 5GT4 A 118 164 UNP P11473 VDR_HUMAN 118 164 DBREF 5GT4 A 216 423 UNP P11473 VDR_HUMAN 216 423 SEQRES 1 A 255 ASP SER LEU ARG PRO LYS LEU SER GLU GLU GLN GLN ARG SEQRES 2 A 255 ILE ILE ALA ILE LEU LEU ASP ALA HIS HIS LYS THR TYR SEQRES 3 A 255 ASP PRO THR TYR SER ASP PHE CYS GLN PHE ARG PRO PRO SEQRES 4 A 255 VAL ARG VAL ASN ASP GLY GLY GLY SER VAL THR LEU GLU SEQRES 5 A 255 LEU SER GLN LEU SER MET LEU PRO HIS LEU ALA ASP LEU SEQRES 6 A 255 VAL SER TYR SER ILE GLN LYS VAL ILE GLY PHE ALA LYS SEQRES 7 A 255 MET ILE PRO GLY PHE ARG ASP LEU THR SER GLU ASP GLN SEQRES 8 A 255 ILE VAL LEU LEU LYS SER SER ALA ILE GLU VAL ILE MET SEQRES 9 A 255 LEU ARG SER ASN GLU SER PHE THR MET ASP ASP MET SER SEQRES 10 A 255 TRP THR CYS GLY ASN GLN ASP TYR LYS TYR ARG VAL SER SEQRES 11 A 255 ASP VAL THR LYS ALA GLY HIS SER LEU GLU LEU ILE GLU SEQRES 12 A 255 PRO LEU ILE LYS PHE GLN VAL GLY LEU LYS LYS LEU ASN SEQRES 13 A 255 LEU HIS GLU GLU GLU HIS VAL LEU LEU MET ALA ILE CYS SEQRES 14 A 255 ILE VAL SER PRO ASP ARG PRO GLY VAL GLN ASP ALA ALA SEQRES 15 A 255 LEU ILE GLU ALA ILE GLN ASP ARG LEU SER ASN THR LEU SEQRES 16 A 255 GLN THR TYR ILE ARG CYS ARG HIS PRO PRO PRO GLY SER SEQRES 17 A 255 HIS LEU LEU TYR ALA LYS MET ILE GLN LYS LEU ALA ASP SEQRES 18 A 255 LEU ARG SER LEU ASN GLU GLU HIS SER LYS GLN TYR ARG SEQRES 19 A 255 CYS LEU SER PHE GLN PRO GLU CYS SER MET LYS LEU THR SEQRES 20 A 255 PRO LEU VAL LEU GLU VAL PHE GLY HET 2KB A 501 36 HETNAM 2KB 4-{[(1R,2S,3R,5Z,7E,14BETA,17ALPHA)-1,3,25-TRIHYDROXY- HETNAM 2 2KB 9,10-SECOCHOLESTA-5,7,10-TRIEN-2-YL]OXY}BUTANENITRILE FORMUL 2 2KB C31 H49 N O4 FORMUL 3 HOH *71(H2 O) HELIX 1 AA1 SER A 125 TYR A 143 1 19 HELIX 2 AA2 ASP A 149 PHE A 153 5 5 HELIX 3 AA3 SER A 216 LEU A 224 1 9 HELIX 4 AA4 MET A 226 MET A 247 1 22 HELIX 5 AA5 GLY A 250 LEU A 254 5 5 HELIX 6 AA6 THR A 255 SER A 275 1 21 HELIX 7 AA7 ASN A 290 ASP A 292 5 3 HELIX 8 AA8 ARG A 296 LYS A 302 1 7 HELIX 9 AA9 SER A 306 LEU A 323 1 18 HELIX 10 AB1 HIS A 326 VAL A 339 1 14 HELIX 11 AB2 ASP A 348 HIS A 371 1 24 HELIX 12 AB3 LEU A 378 PHE A 406 1 29 HELIX 13 AB4 GLU A 409 LEU A 414 1 6 HELIX 14 AB5 THR A 415 GLY A 423 1 9 SHEET 1 AA1 3 PHE A 279 THR A 280 0 SHEET 2 AA1 3 SER A 285 THR A 287 -1 O SER A 285 N THR A 280 SHEET 3 AA1 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 -9.43 CISPEP 2 PRO A 373 PRO A 374 0 -0.13 SITE 1 AC1 15 TYR A 143 ASP A 144 TYR A 147 PHE A 150 SITE 2 AC1 15 LEU A 227 LEU A 233 VAL A 234 SER A 237 SITE 3 AC1 15 ARG A 274 SER A 275 SER A 278 TRP A 286 SITE 4 AC1 15 HIS A 305 HIS A 397 HOH A 658 CRYST1 44.663 51.842 131.475 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 0.022390 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007606 0.00000