PDB entry 4ei5

View 4ei5 on RCSB PDB site
Description: Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1
Class: immune system
Keywords: sulfatide, lipid, CD1d, NKT typeII, TCR, IMMUNE SYSTEM
Deposited on 2012-04-04, released 2012-07-25
The last revision prior to the SCOPe 2.07 freeze date was dated 2012-09-05, with a file datestamp of 2012-08-31.
Experiment type: XRAY
Resolution: 3.1 Å
R-factor: 0.199
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, Cd1.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • see remark 999 (200)
      • expression tag (279-300)
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (Start-98)
      • see remark 999 (84)
    Domains in SCOPe 2.07: d4ei5b_
  • Chain 'C':
    Compound: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.07: d4ei5c1, d4ei5c2
  • Chain 'D':
    Compound: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.07: d4ei5d1, d4ei5d2
  • Chain 'E':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, Cd1.1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • expression tag (279-289)
    Domains in SCOPe 2.07: d4ei5e1, d4ei5e2, d4ei5e3
  • Chain 'F':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887
      • see remark 999 (84)
    Domains in SCOPe 2.07: d4ei5f_
  • Chain 'G':
    Compound: Valpha1 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.07: d4ei5g1
  • Chain 'H':
    Compound: Vbeta16 XV19 Type II Natural Killer T cell receptor (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 4EI5
    Domains in SCOPe 2.07: d4ei5h1, d4ei5h2
  • Heterogens: NAG, FLC, CIS

PDB Chain Sequences:

  • Chain 'A':
    No sequence available.

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4ei5B (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ei5B (B:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4ei5C (C:)
    mqqkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkeg
    rftahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpd
    pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
    nksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ei5C (C:)
    qkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkegrf
    tahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpdpa
    vyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsnk
    sdfacanafnnsiipedtffp
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4ei5D (D:)
    mgpkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmeksk
    lfkdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlkn
    vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ei5D (D:)
    pkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmeksklf
    kdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlknvf
    ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
    alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
    ra
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4ei5E (E:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhrhhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ei5E (E:)
    nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
    qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
    rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
    ekpvawlssvpghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqat
    ldveageeaglacrvkhsslggqdiilywgslhhildaqk
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4ei5F (F:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ei5F (F:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhasmaepktvywd
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4ei5G (G:)
    mqqkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkeg
    rftahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpd
    pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
    nksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ei5G (G:)
    qkvqqspeslsvpeggmaslnctssdrnfqyfwwyrqhsgegpkalmsifsdgdkkegrf
    tahlnkaslhvslhirdsqpsdsalyfcaaseqnnyaqgltfglgtrvsvfpyiqnpdpa
    vyqlftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsnsiipedtffp
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4ei5H (H:)
    mgpkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmeksk
    lfkdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlkn
    vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >4ei5H (H:)
    gpkvlqipshqiidmgqmvtlncdpvsnhlyfywykqilgqqmeflvnfyngkvmekskl
    fkdqfsverpdgsyftlkiqptaledsavyfcassfwgayaeqffgpgtrltvledlknv
    fppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqpndsr
    yalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsa