PDB entry 6mjq

View 6mjq on RCSB PDB site
Description: Crystal structure of the mCD1d/xxp (JJ295) /iNKTCR ternary complex
Class: immune system/inhibitor
Keywords: MHC-fold, Ig-fold, glycolipid antigen presentation, T cell receptor, IMMUNE SYSTEM, immune system-inhibitor complex
Deposited on 2018-09-21, released 2019-01-09
The last revision prior to the SCOPe 2.07 freeze date was dated 2019-01-16, with a file datestamp of 2019-01-11.
Experiment type: XRAY
Resolution: 3 Å
R-factor: N/A
AEROSPACI score: 0.14 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, mCG_3074
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6mjqa1, d6mjqa2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6mjqb_
  • Chain 'C':
    Compound: T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A0B4J1J9 (1-92)
      • linker (113)
    • PDB 6MJQ (93-112)
    • Uniprot K7N5M3 (114-End)
    Domains in SCOPe 2.07: d6mjqc1, d6mjqc2
  • Chain 'D':
    Compound: Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
    Species: Homo sapiens [TaxId:9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • Uniprot A2NTY6 (Start-94)
      • linker (95-98)
    • Uniprot A0N8J3 (99-130)
      • linker (130)
    • Uniprot A0A5B9 (131-240)
      • variant (168)
      • variant (186)
    Domains in SCOPe 2.07: d6mjqd1, d6mjqd2
  • Chain 'E':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, mCG_3074
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6mjqe1, d6mjqe2
  • Chain 'F':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6mjqf_
  • Chain 'G':
    Compound: T cell receptor alpha variable 11,T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A0B4J1J9 (Start-92)
      • linker (113)
    • PDB 6MJQ (93-112)
    • Uniprot K7N5M3 (114-End)
    Domains in SCOPe 2.07: d6mjqg1, d6mjqg2
  • Chain 'H':
    Compound: Beta-chain,T cell receptor chain,T cell receptor beta constant 2, CHIMERIC PROTEIN
    Species: Homo sapiens [TaxId:9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • Uniprot A2NTY6 (Start-94)
      • linker (95-98)
    • Uniprot A0N8J3 (99-130)
      • linker (130)
    • Uniprot A0A5B9 (131-240)
      • variant (168)
      • variant (186)
    Domains in SCOPe 2.07: d6mjqh1, d6mjqh2
  • Heterogens: GOL, NA, NAG, FUC, BMA, JUD, MAN, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6mjqA (A:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqA (A:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetw
    ylqatldveageeaglacrvkhsslggqdiilyw
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6mjqB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqB (B:)
    ktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdwsf
    yilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6mjqC (C:)
    mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
    grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqC (C:)
    ktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsng
    rysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpd
    pavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaws
    nfacanafnnsiipedtffps
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6mjqD (D:)
    meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
    ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
    pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    a
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqD (D:)
    eaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdi
    pdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtpp
    kvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpal
    ndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6mjqE (E:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqE (E:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetw
    ylqatldveageeaglacrvkhsslggqdiilyw
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6mjqF (F:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqF (F:)
    ktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdwsf
    yilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >6mjqG (G:)
    mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
    grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqG (G:)
    tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    dfacanafnnsiipedtffps
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >6mjqH (H:)
    meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
    ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
    pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    a
    

    Sequence, based on observed residues (ATOM records): (download)
    >6mjqH (H:)
    aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
    dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
    vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
    dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra