PDB entry 3vwj

View 3vwj on RCSB PDB site
Description: Ternary crystal structure of the human NKT TCR-CD1d-C20:2 complex
Class: immune system
Keywords: cd1d, nkt t cell receptor, alpha-galactosylceramide, protein receptor complex, cell membrane, disulfide bond, endosome, glycoprotein, host-virus interaction, immune response, immunoglobulin domain, innate immunity, lysosome, membrane, transmembrane, disease mutation, glycation, MHC I, pyrrolidone carboxylic acid, secreted, immune system
Deposited on 2012-08-24, released 2012-10-03
The last revision prior to the SCOPe 2.06 freeze date was dated 2013-08-14, with a file datestamp of 2013-08-09.
Experiment type: XRAY
Resolution: 3.09 Å
R-factor: 0.231
AEROSPACI score: 0.18 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-277)
      • expression tag (278)
    Domains in SCOPe 2.06: d3vwja1, d3vwja2, d3vwja3
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3vwjb_
  • Chain 'C':
    Compound: NKT15 T cell receptor alpha-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3VWJ
    Domains in SCOPe 2.06: d3vwjc1, d3vwjc2
  • Chain 'D':
    Compound: NKT15 T cell receptor beta-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3VWJ
    Domains in SCOPe 2.06: d3vwjd1, d3vwjd2
  • Heterogens: NAG, DB3, MG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3vwjA (A:)
    spgvpqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgks
    elkkqvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpna
    detwylratldvvageaaglscrvkhsslegqdivlywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vwjA (A:)
    fplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwetlq
    hifrvyrssftrdvkefakmlrlsyplelqvsagcevsnnffhvafqgkdilsfqgtswe
    ptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqvkpkawls
    rgpspgrlllvchvsgfypkpvwvkwmeqqgtqpgdilpnadetwylratldvscrvkhs
    slegqdivlywh
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3vwjB (B:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vwjB (B:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3vwjC (C:)
    mknqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksn
    grytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vwjC (C:)
    nqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngr
    ytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdinpdpa
    vyqlrdssvclftdfdsqtnvsqsksdvyitdkcvldmrsmdfksnsavawsdfacanaf
    nnsiipedtffps
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3vwjD (D:)
    meadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgd
    lssestvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlk
    nvfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplk
    eqpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsae
    awgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >3vwjD (D:)
    diyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdlss
    estvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlknvf
    ppevavfepseaeishtqkatlvclatgfypdhvelswwvnkevhsgvctdpqplkeqpa
    lndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    a