PDB entry 3sdd

View 3sdd on RCSB PDB site
Description: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-beta-lactosylceramide
Class: immune system
Keywords: CD1d, autoimmunity, self-recognition, NKT, IMMUNE SYSTEM
Deposited on 2011-06-09, released 2011-10-05
The last revision prior to the SCOPe 2.07 freeze date was dated 2011-10-05, with a file datestamp of 2011-09-30.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.261
AEROSPACI score: 0.19 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1.1, Cd1d1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • see remark 999 (200)
      • expression tag (279-294)
    Domains in SCOPe 2.07: d3sdda1, d3sdda2, d3sdda3
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (0-98)
      • see remark 999 (84)
    Domains in SCOPe 2.07: d3sddb_
  • Chain 'C':
    Compound: NKT TCR Valpha14 chain
    Species: Mus musculus , Homo sapiens [TaxId:10090, 9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDD (0-End)
    Domains in SCOPe 2.07: d3sddc1, d3sddc2
  • Chain 'D':
    Compound: NKT TCR autoreactive-Vbeta6 chain
    Species: Mus musculus , Homo sapiens [TaxId:10090, 9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 3SDD
    Domains in SCOPe 2.07: d3sddd1, d3sddd2
  • Heterogens: NAG, 3GD, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3sddA (A:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnhrhhhh
    hh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sddA (A:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetw
    ylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnh
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >3sddB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3sddC (C:)
    tqveqspqslvvrqgensvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    ksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sddC (C:)
    tqveqspqslvvrqgensvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdsksclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawscanafn
    nsiipedtf
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3sddD (D:)
    hmggiitqtpkfligqegqkltlkcqqnfnhdtmywyrqdsgkglrliyysygagstekg
    dlsegydasrekkssfsltvtsaqknemavflcasgslldvrevffgkgtrltvvedlkn
    vfppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad
    

    Sequence, based on observed residues (ATOM records): (download)
    >3sddD (D:)
    ggiitqtpkfligqegqkltlkcqqnfnhdtmywyrqdsgkglrliyysygagstekgdl
    segydasrekkssfsltvtsaqknemavflcasgslldvrevffgkgtrltvvedlknvf
    ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
    alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea