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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN VITAMIN D RECEPTOR LIGAND BINDING DOMAIN COMPLEXED WITH 1ALPHA,25-DIHYDROXY-2ALPHA-[2-(1H-TETRAZOLE-1-YL)ETHYL]VITAMIN D3
 
Authors :  S. Kakuda, M. Takimoto-Kamimura
Date :  18 Jan 13  (Deposition) - 22 Jan 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym./Biol. Unit :  A
Keywords :  Hormone Receptor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Matsuo, A. Hasegawa, M. Takano, H. Saito, S. Kakuda, T. Chida, K. Takagi, E. Ochiai, K. Horie, Y. Harada, M. Takimoto-Kamimura, K. Takenouchi, D. Sawada, A. Kittaka
Synthesis Of 2 Alpha-Heteroarylalkyl Active Vitamin D3 With Therapeutic Effect On Enhancing Bone Mineral Density In Viv
Acs Med. Chem. Lett. V. 4 671 2013
PubMed-ID: 24900728  |  Reference-DOI: 10.1021/ML400098W

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGAND BINDING DOMAIN, RESIDUES 118-427
    Gene: VDR
    Mutation: YES
    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
1TFY1Ligand/Ion(1R,2S,3S,5Z)-5-[(2E)-2-[(1R,3AS,7AR)-7A-METHYL-1-[(2R)-6-METHYL-6-OXIDANYL-HEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLIDENE]-4-METHYLIDENE-2-[2-(1,2,3,4-TETRAZOL-1-YL)ETHYL]CYCLOHEXANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:142 , TYR A:143 , ASP A:144 , LEU A:227 , LEU A:233 , VAL A:234 , TYR A:236 , SER A:237 , ILE A:271 , ARG A:274 , SER A:275 , SER A:278 , TRP A:286 , CYS A:288 , HIS A:305 , LEU A:309 , HIS A:397BINDING SITE FOR RESIDUE TFY A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ITF)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:289 -Asn A:290
2Pro A:372 -Pro A:373
3Pro A:373 -Pro A:374

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ITF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ITF)

(-) Exons   (0, 0)

(no "Exon" information available for 4ITF)

(-) 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains d4itfa_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....hhhhh..........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...ee....eee..hhh.eehhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4itf A 118 DSLRPKLSEEQQRIIAILLDAHHKTYDPTYSDFCQFRPPVRVNDGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEVFG 423
                                   127       137       147       157    || 220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420   
                                                                      162|                                                                                                                                                                                                               
                                                                       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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ITF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ITF)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  VDR_HUMAN | P11473
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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 5gt4

(-) Related Entries Specified in the PDB File

4ite