PDB entry 4y2d

View 4y2d on RCSB PDB site
Description: Crystal structure of the mCD1d/7DW8-5/iNKTCR ternary complex
Class: immune system
Keywords: MHC-fold, Ig-fold, glycolipid antigen presentation, T cell receptor, IMMUNE SYSTEM
Deposited on 2015-02-09, released 2015-05-27
The last revision prior to the SCOPe 2.05 freeze date was dated 2015-05-27, with a file datestamp of 2015-05-22.
Experiment type: XRAY
Resolution: 3.05 Å
R-factor: N/A
AEROSPACI score: 0.13 (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): Domains in SCOPe 2.05: d4y2da1
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4y2db_
  • Chain 'C':
    Compound: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Gene: Trav11, Trav11d, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y2D
    Domains in SCOPe 2.05: d4y2dc1, d4y2dc2
  • Chain 'D':
    Compound: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y2D (Start-240)
    Domains in SCOPe 2.05: d4y2dd1, d4y2dd2
  • Chain 'E':
    Compound: Antigen-presenting glycoprotein CD1d1
    Species: Mus musculus [TaxId:10090]
    Gene: Cd1d1, Cd1.1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4y2de1
  • Chain 'F':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.05: d4y2df_
  • Chain 'G':
    Compound: Chimeric TCR Valpha14/Jalpha18 chain (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Gene: Trav11, Trav11d, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y2D
    Domains in SCOPe 2.05: d4y2dg1, d4y2dg2
  • Chain 'H':
    Compound: Chimeric TCR Vbeta8.2 chain (mouse variable domain, human constant domain)
    Species: Mus musculus, Homo sapiens [TaxId:10090, 9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • PDB 4Y2D (Start-240)
    Domains in SCOPe 2.05: d4y2dh1, d4y2dh2
  • Heterogens: NAG, 7DW, FU4

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4y2dA (A:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dA (A:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpqlvchvsgfypkpvwvthrgdflpnadetwylqatldgeeaglacrvk
    hsslggqdi
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4y2dB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdr
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4y2dC (C:)
    mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
    grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dC (C:)
    tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    kdfacanafnnsiipedtffps
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4y2dD (D:)
    meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
    ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
    pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    a
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dD (D:)
    aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
    dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
    vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
    dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >4y2dE (E:)
    seaqqknytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsn
    qqweklqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvaf
    qgkyvvrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagk
    sdlekqekpvawlssvpssahghrqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpn
    adetwylqatldveageeaglacrvkhsslggqdiilywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dE (E:)
    knytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwek
    lqhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyv
    vrfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlek
    qekpvawlssvpqlvchvsgfypkpvwvmeqqgthrgdflpnadetwylqcrvkhsslgg
    qdi
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >4y2dF (F:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dF (F:)
    qktpqiqvysrhppelncyvtqfhpphieiqmlkngkkipkvemsdmsfskdwsfyilah
    teftptetdtcrvkhasmaepktvywdr
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >4y2dG (G:)
    mktqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsn
    grysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnp
    dpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavaw
    snksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dG (G:)
    tqveqspqslvvrqgencvlqcnysvtpdnhlrwfkqdtgkglvsltvlvdqkdktsngr
    ysatldkdakhstlhitatllddtatyicvvgdrgsalgrlhfgagtqlivipdiqnpdp
    avyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsavawsn
    kdfacanafnnsiipedtffps
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >4y2dH (H:)
    meaavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgd
    ipdgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtp
    pkvslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpa
    lndsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgr
    a
    

    Sequence, based on observed residues (ATOM records): (download)
    >4y2dH (H:)
    aavtqsprnkvavtggkvtlscnqtnnhnnmywyrqdtghglrlihysygagstekgdip
    dgykasrpsqenfslilelatpsqtsvyfcasgdegytqyfgpgtrllvledlrnvtppk
    vslfepskaeishtqkatlvclatgfypdhvelswwvngkevhsgvctdpqplkeqpaln
    dsryslssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaeawgra