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(-) Description

Title :  CRYSTAL STRUCTURE OF VDR IN COMPLEX WITH DLAM-4 (C2 FORM)
 
Authors :  L. Asano, T. Shimizu
Date :  23 Jun 16  (Deposition) - 07 Dec 16  (Release) - 07 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Nuclear Receptor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Asano, T. Waku, R. Abe, N. Kuwabara, I. Ito, J. Yanagisawa, K. Nagasawa, T. Shimizu
Regulation Of The Vitamin D Receptor By Vitamin D Lactam Derivatives.
Febs Lett. V. 590 3270 2016
PubMed-ID: 27500498  |  Reference-DOI: 10.1002/1873-3468.12348

(-) Compounds

Molecule 1 - VITAMIN D3 RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 124-164,UNP RESIDUES 212-419
    Gene: VDR, NR1I1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: VDR,1,25-DIHYDROXYVITAMIN D3 RECEPTOR,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP I MEMBER 1
 
Molecule 2 - SRC1
    Chains: C
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1VDP1Ligand/Ion(3R,5S)-5-[(2R)-2-[(1R,3AS,4E,7AR)-7A-METHYL-4-[(2Z)-2-[(3S,5R)-2-METHYLIDENE-3,5-BIS(OXIDANYL)CYCLOHEXYLIDENE]ETHYLIDENE]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-1-YL]PROPYL]-3-METHYL-3-OXIDANYL-1-(4-PHENYLBUTYL)PYRROLIDIN-2-ONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:143 , LEU A:220 , SER A:233 , ILE A:267 , ARG A:270 , SER A:271 , SER A:274 , TRP A:282 , THR A:302 , HIS A:393 , TYR A:397 , PHE A:418binding site for residue VDP A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:369 -Pro A:370

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GID)

(-) 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:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...ee....eee......eehhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gid A 124 LSEEQQHIIAILLDAHHKTYDPTYADFRDFRPPVRMPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFG 419
                                   133       143       153     ||222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       
                                                             159|                                                                                                                                                                                                        
                                                              219                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5gid C 626 NHPMLMNLL 634
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5GID)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (126, 133)

Asymmetric/Biological Unit(hide GO term definitions)

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  5gid
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  MED1_HUMAN | Q15648
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  VDR_RAT | P13053
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 Related Entries

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

UniProtKB/Swiss-Prot
        MED1_HUMAN | Q15648: 1rjk 1rk3 1rkg 1rkh 2o4j 2o4r 2zfx 3a2h 3aun 3vjs 3vjt 3vrt 3vru 3vrv 3vrw 3w0g 3w0h 3w0i 3w0j 3w5p 3w5q 3w5r 3w5t 3wt5 3wt6 3wt7 3wtq 4ynk 5awj 5awk 5b41 5b5b 5gic 5gie
        VDR_RAT | P13053: 1rjk 1rk3 1rkg 1rkh 2o4j 2o4r 2zfx 2zl9 2zla 2zlc 2zmh 2zmi 2zmj 2zxm 2zxn 3a2h 3afr 3aun 3vjs 3vjt 3vrt 3vru 3vrv 3vrw 3vt3 3vt4 3vt5 3vt6 3vt7 3vt8 3vt9 3vtb 3vtc 3vtd 3w0g 3w0h 3w0i 3w0j 3w5p 3w5q 3w5r 3w5t 3wt5 3wt6 3wt7 3wtq 4ynk 5awj 5awk 5b41 5b5b 5gic 5gie 5h1e

(-) Related Entries Specified in the PDB File

5gic 5gie