PDB entry 3scm

View 3scm on RCSB PDB site
Description: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-isoglobotrihexosylceramide
Class: immune system
Keywords: Ternary Complex, Immunity, APC Cell surface, IMMUNE SYSTEM
Deposited on 2011-06-08, 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: 2.5 Å
R-factor: 0.275
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 (279-294)
    Domains in SCOPe 2.07: d3scma1, d3scma2, d3scma3
  • 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: d3scmb_
  • Chain 'C':
    Compound: NKT TCR Valpha14 chain
    Species: Mus musculus , Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SCM (0-End)
    Domains in SCOPe 2.07: d3scmc1, d3scmc2
  • Chain 'D':
    Compound: NKT TCR autoreactive-Vbeta6 chain
    Species: Mus musculus , Homo sapiens [TaxId:10090, 9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3SCM
    Domains in SCOPe 2.07: d3scmd1, d3scmd2
  • Heterogens: NAG, LGN, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >3scmA (A:)
    nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
    qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
    rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
    ekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwy
    lqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnh
    

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

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

    Sequence, based on observed residues (ATOM records): (download)
    >3scmC (C:)
    tqveqspqslvvrqgensvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsacan
    afnnipedtff
    

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

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