PDB entry 3vwk

View 3vwk on RCSB PDB site
Description: Ternary crystal structure of the human NKT TCR-CD1d-4'deoxy-alpha-galactosylceramide 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 2.07 freeze date was dated 2013-08-14, with a file datestamp of 2013-08-09.
Experiment type: XRAY
Resolution: 2.94 Å
R-factor: 0.194
AEROSPACI score: 0.26 (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): Domains in SCOPe 2.07: d3vwka1, d3vwka2
  • 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 2.07: d3vwkb_
  • Chain 'C':
    Compound: NKT15 T cell receptor alpha-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3VWK
    Domains in SCOPe 2.07: d3vwkc1, d3vwkc2
  • Chain 'D':
    Compound: NKT15 T cell receptor beta-chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3VWK
    Domains in SCOPe 2.07: d3vwkd1, d3vwkd2
  • Heterogens: NAG, 4GH, MG, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >3vwkA (A:)
    lfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwetl
    qhifrvyrssftrdvkefakmlrlsyplelqvsagcevhnnffhvafqgkdilsfqgtsw
    eptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqvkpkawl
    srgpspgrlllvchvsgfypkpvwvkwmtqpgdilpnadetwylratldvlscrvkhssl
    egqdivlyw
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3vwkB (B:)
    qrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdws
    fyllyyteftptekdeyacrvnhvtlsqpkivkwdr
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3vwkC (C:)
    qveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngry
    tatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdpa
    vyqlrdssvclftdfdsqtnvsqsdsdvyitdkcvldmrsmdfksnsavawsnksdfaca
    nafnnsiipedtff
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >3vwkD (D:)
    diyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdlss
    estvsrirtehfpltlesarpshtsqylcassglrdrglyeqyfgpgtrltvtedlknvf
    ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
    alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
    ra