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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND BINDING DOMAIN COMPLEXED WITH 7,8-CIS-14-EPI-1A,25-DIHYDROXY-19-NORVITAMIN D3
 
Authors :  S. Kakuda, M. Takimoto-Kamimura
Date :  13 Jan 15  (Deposition) - 13 Jan 16  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A
Keywords :  Hormone Receptor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Sawada, H. Saito, S. Kakuda, M. Takimoto-Kamimura, Y. Matsumoto, K. Takagi, E. Ochiai, A. Kittaka
Revisiting The 7, 8-Cis-Vitamin D3 Derivatives: Synthesis, Evaluating The Biological Activity, And Study Of The Bindin Configuration
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentLIGAND BINDING DOMAIN (UNP RESIDUES 118-164, 216-427)
    GeneNR1I1, VDR
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymVDR, 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
141V1Ligand/Ion(1R,3R,7Z,14BETA,17ALPHA)-17-[(2R)-6-HYDROXY-6-METHYLHEPTAN-2-YL]-9,10-SECOESTRA-5,7-DIENE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:143 , LEU A:227 , VAL A:234 , SER A:237 , ARG A:274 , SER A:275 , SER A:278 , TRP A:286 , VAL A:300 , HIS A:305 , HIS A:397BINDING SITE FOR RESIDUE 41V A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X31)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:288 -Gly A:289
2Pro A:373 -Pro A:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3X31)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X31)

(-) Exons   (0, 0)

(no "Exon" information available for 3X31)

(-) 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    
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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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....hhhhh...........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee..hhh.eehhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x31 A 118 DSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG 423
                                   127       137       147       157     ||219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419    
                                                                       163|                                                                                                                                                                                                               
                                                                        216                                                                                                                                                                                                               

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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 3X31)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X31)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X31)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        VDR_HUMAN | P114731db1 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 3x36 4g2i 4ite 4itf 5gt4

(-) Related Entries Specified in the PDB File

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