PDB entry 4zak

View 4zak on RCSB PDB site
Description: Crystal structure of the mCD1d/DB06-1/iNKTCR ternary complex
Class: immune system
Keywords: MHC-fold, Ig-fold, glycolipid antigen presentation, T cell receptor, IMMUNE SYSTEM
Deposited on 2015-04-13, released 2015-07-01
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-09-06, with a file datestamp of 2017-09-01.
Experiment type: XRAY
Resolution: 2.82 Å
R-factor: N/A
AEROSPACI score: 0.16 (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 2.07: d4zaka1, d4zaka2
  • 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: d4zakb_
  • Chain 'C':
    Compound: Protein Trav11,Va14Ja18/Vb8.2,Human nkt tcr alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A0B4J1J9 (Start-93)
    • Uniprot A0N4Z0 (94-112)
      • conflict (98)
      • conflict (103)
      • conflict (106)
      • conflict (111)
      • linker (113)
    • Uniprot K7N5M3 (114-End)
    Domains in SCOPe 2.07: d4zakc1, d4zakc2
  • Chain 'D':
    Compound: T cell antigen receptor beta chain 8.2,T-cell receptor beta-2 chain C region,Protein Trbc2,T-cell receptor beta-2 chain C region
    Species: Homo sapiens [TaxId:9606]
    Gene: TRBC2, TCRBC2
    Database cross-references and differences (RAF-indexed):
    • PDB 4ZAK (Start-112)
    • Uniprot A0A075B5J4 (113-129)
    • Uniprot A0A5B9 (130-240)
      • engineered mutation (168)
      • engineered mutation (186)
    Domains in SCOPe 2.07: d4zakd1, d4zakd2
  • Heterogens: NAG, 4LX

PDB Chain Sequences:

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

    Sequence, based on observed residues (ATOM records): (download)
    >4zakA (A:)
    nytfrclqmssfanrswsrtdsvvwlgdlqthrwsndsatisftkpwsqgklsnqqwekl
    qhmfqvyrvsftrdiqelvkmmspkedypieiqlsagcemypgnasesflhvafqgkyvv
    rfwgtswqtvpgapswldlpikvlnadqgtsatvqmllndtcplfvrglleagksdlekq
    ekpvawlssvprqlvchvsgfypkpvwvmwmrgdqeqqgthrgdflpnadetwylqatld
    veageeaglacrvkhsslggqdiilyw
    

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

    Sequence, based on observed residues (ATOM records): (download)
    >4zakB (B:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhasmaepktvywdrdm
    

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

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

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

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