PDB entry 3sdx

View 3sdx on RCSB PDB site
Description: Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with CD1d-beta-galactosylceramide
Class: immune system
Keywords: CD1d, autoimmunity, self-recognition, NKT, extracellular, IMMUNE SYSTEM
Deposited on 2011-06-09, released 2011-10-05
The last revision prior to the SCOPe 2.06 freeze date was dated 2011-10-05, with a file datestamp of 2011-09-30.
Experiment type: XRAY
Resolution: 3.12 Å
R-factor: 0.234
AEROSPACI score: 0.19 (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 (0-271)
      • expression tag (272-274)
    Domains in SCOPe 2.06: d3sdxa1, d3sdxa2, d3sdxa3
  • 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: d3sdxb_
  • Chain 'C':
    Compound: Antigen-presenting glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d3sdxc1, d3sdxc2
  • Chain 'D':
    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: d3sdxd_
  • Chain 'E':
    Compound: NKT TCR Valpha24 chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDX (0-End)
    Domains in SCOPe 2.06: d3sdxe1, d3sdxe2
  • Chain 'F':
    Compound: NKT TCR autoreactive-Vbeta11 chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDX (Start-246)
    Domains in SCOPe 2.06: d3sdxf1, d3sdxf2
  • Chain 'G':
    Compound: NKT TCR Valpha24 chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDX (0-End)
    Domains in SCOPe 2.06: d3sdxg1, d3sdxg2
  • Chain 'H':
    Compound: NKT TCR autoreactive-Vbeta11 chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDX (0-246)
    Domains in SCOPe 2.06: d3sdxh1, d3sdxh2
  • Heterogens: GCY, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3sdxA (A:)
    rlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqv
    kpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwyl
    ratldvvageaaglscrvkhsslegqdivlywhhh
    

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

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

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3sdxC (C:)
    rlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqv
    kpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwyl
    ratldvvageaaglscrvkhsslegqdivlywhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sdxC (C:)
    rlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqv
    kpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwyl
    ratldvvagescrvkhsslegqdivlyw
    

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

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

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3sdxE (E:)
    nqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngr
    ytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    ksdfacanafnnsiipedtffpsp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sdxE (E:)
    nqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngr
    ytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdp
    avyqlrdssvclftdfdsqtnvsqssdvyitdkcvldmrsmdfksnsavawsnksdfaca
    nafnnsiipedtffps
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3sdxF (F:)
    eadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdl
    ssestvsrirtehfpltlesarpshtsqylcassefggtertqetqyfgpgtrllvledl
    knvfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqpl
    keqpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsa
    eawgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sdxF (F:)
    adiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdls
    sestvsrirtehfpltlesarpshtsqylcassefgtqetqyfgpgtrllvledlknvfp
    pevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    ad
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >3sdxG (G:)
    nqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngr
    ytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    ksdfacanafnnsiipedtffpsp
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sdxG (G:)
    nqveqspqsliilegknctlqcnytvspfsnlrwykqdtgrgpvsltimtfsentksngr
    ytatldadtkqsslhitasqlsdsasyicvvsdrgstlgrlyfgrgtqltvwpdiqnpdp
    avyqlrdssvclftdfdsqtnvsqssdvyitdkcvldmrsmdfksnsavawsnksdfaca
    nafnnsiipedtffps
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >3sdxH (H:)
    eadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgdl
    ssestvsrirtehfpltlesarpshtsqylcassefggtertqetqyfgpgtrllvledl
    knvfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqpl
    keqpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsa
    eawgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sdxH (H:)
    eadiyqtprylvigtgkkitlecsqtmghdkmywyqqdpgmelhlihysygvnstekgss
    estvsrirtehfpltlesarpshtsqylcasseftqetqyfgpgtrllvledlknvfppe
    vavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
    dsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgrad