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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND BINDING DOMAIN COMPLEXED WITH (1R,2S,3R,5Z,7E,14BETA,17ALPHA)-2-CYANOPROPOXY-9,10-SECOCHOLESTA-5,7,10-TRIENE-1,3,25-TRIOL
 
Authors :  M. Takimoto-Kamimura
Date :  18 Aug 16  (Deposition) - 09 Nov 16  (Release) - 09 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A
Keywords :  Nuclear Hormone Receptor Full Agonist Ligand Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Takimoto-Kamimura
Crystal Structure Of The Human Vitamin D Receptor Ligand Binding Domain Complexed With (1R, 2S, 3R, 5Z, 7E, 14Beta, 17Alpha)-2-Cyanopropoxy-9, 10-Secocholesta-5, 7, 10-Triene-1, 3, 25-Triol
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 118-164,216-423
    Gene: VDR, NR1I1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
12KB1Ligand/Ion4-{[(1R,2S,3R,5Z,7E,14BETA,17ALPHA)-1,3,25-TRIHYDROXY-9,10-SECOCHOLESTA-5,7,10-TRIEN-2-YL]OXY}BUTANENITRILE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:143 , ASP A:144 , TYR A:147 , PHE A:150 , LEU A:227 , LEU A:233 , VAL A:234 , SER A:237 , ARG A:274 , SER A:275 , SER A:278 , TRP A:286 , HIS A:305 , HIS A:397 , HOH A:658binding site for residue 2KB A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GT4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:372 -Pro A:373
2Pro A:373 -Pro A:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GT4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GT4)

(-) Exons   (0, 0)

(no "Exon" information available for 5GT4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....hhhhh...........hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee..hhh.eehhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gt4 A 118 DSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG 423
                                   127       137       147       157      |218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418     
                                                                        164|                                                                                                                                                                                                               
                                                                         216
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5GT4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GT4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GT4)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  5gt4
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        VDR_HUMAN | P11473: 1db1 1ie8 1ie9 1kb2 1kb4 1kb6 1s0z 1s19 1txi 1ynw 2ham 2har 2has 2hb7 2hb8 3a2i 3a2j 3a3z 3a40 3a78 3auq 3aur 3ax8 3az1 3az2 3az3 3b0t 3cs4 3cs6 3kpz 3m7r 3ogt 3p8x 3tkc 3vhw 3w0a 3w0c 3w0y 3wgp 3wwr 3x31 3x36 4g2i 4ite 4itf

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