PDB entry 4apq

View 4apq on RCSB PDB site
Description: Crystal structure of autoreactive-Valpha14-Vbeta6 NKT TCR in complex with CD1d-sulfatide
Class: immune system
Keywords: immunity, apc cell surface, immune system
Deposited on 2012-04-05, released 2013-04-24
The last revision prior to the SCOPe 2.07 freeze date was dated 2013-04-24, with a file datestamp of 2013-04-19.
Experiment type: XRAY
Resolution: 3 Å
R-factor: 0.1802
AEROSPACI score: 0.26 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P11609 (Start-278)
      • variant (200)
      • expression tag (279-294)
    Domains in SCOPe 2.07: d4apqa1, d4apqa2, d4apqa3
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (0-98)
      • variant (84)
    Domains in SCOPe 2.07: d4apqb_
  • Chain 'C':
    Compound: mouse nkt tcr valpha14, human nkt tcr valpha14
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 4APQ (116-End)
    Domains in SCOPe 2.07: d4apqc1, d4apqc2
  • Chain 'D':
    Compound: mouse nkt tcr autoreactive-vbeta6, human nkt tcr autoreactive-vbeta6
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 4APQ (117-End)
    Domains in SCOPe 2.07: d4apqd1, d4apqd2
  • Heterogens: CIS, HOH

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >4apqA (A:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetw
    ylqatldveageeaglacrvkhsslggqdiilywgslhhildaqkmvwnh
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >4apqB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4apqC (C:)
    tqveqspqslvvrqgensvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    ksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >4apqC (C:)
    tqveqspqslvvrqgensvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsa
    canafnnsiipedtff
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4apqD (D:)
    ggiitqtpkfligqegqkltlkcqqnfnhdtmywyrqdsgkglrliyysygagstekgdl
    segydasrekkssfsltvtsaqknemavflcasgslldvrevffgkgtrltvvedlknvf
    ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
    alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg
    rad
    

    Sequence, based on observed residues (ATOM records): (download)
    >4apqD (D:)
    ggiitqtpkfligqegqkltlkcqqnfnhdtmywyrqdsgkglrliyysygagstekgdl
    segydasrekkssfsltvtsaqknemavflcasgslldvrevffgkgtrltvvedlknvf
    ppevavfepseaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqp
    alndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawg