PDB entry 6v7z

View 6v7z on RCSB PDB site
Description: Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22
Class: immune system
Keywords: lipid, nanobody, IMMUNE SYSTEM
Deposited on 2019-12-10, released 2020-09-16
The last revision prior to the SCOPe 2.07 freeze date was dated 2020-09-16, with a file datestamp of 2020-09-11.
Experiment type: XRAY
Resolution: 2.75 Å
R-factor: N/A
AEROSPACI score: 0.23 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Antigen-presenting glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (1-274)
      • initiating methionine (0)
    • PDB 6V7Z
    Domains in SCOPe 2.07: d6v7za1, d6v7za2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61769 (1-End)
      • initiating methionine (0)
    Domains in SCOPe 2.07: d6v7zb1, d6v7zb2
  • Chain 'C':
    Compound: Antigen-presenting glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6v7zc1, d6v7zc2
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.07: d6v7zd_
  • Chain 'E':
    Compound: Nanobody VHH ID22
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6V7Z (0-End)
    Domains in SCOPe 2.07: d6v7ze_
  • Chain 'F':
    Compound: Nanobody VHH ID22
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6V7Z (0-End)
    Domains in SCOPe 2.07: d6v7zf_
  • Heterogens: AGH, NAG, PEG, CL, SO4, BGC, NA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6v7zA (A:)
    mqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqw
    etlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdi
    lsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkk
    qvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetw
    ylratldvvageaaglscrvkhsslegqdivlywgslvprgsgsriarleekvktlkaqn
    selastanmlreqvaqlkqkvmnhgsglndifeaqkiewhehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7zA (A:)
    mqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqw
    etlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdi
    lsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkk
    qvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetw
    ylratldvvageaaglscrvkhsslegqdivlywg
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >6v7zB (B:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7zB (B:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrd
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >6v7zC (C:)
    mqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqw
    etlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdi
    lsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkk
    qvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetw
    ylratldvvageaaglscrvkhsslegqdivlywgslvprgsgsriarleekvktlkaqn
    selastanmlreqvaqlkqkvmnhgsglndifeaqkiewhehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7zC (C:)
    rlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgasnnffhvafqgkdilsf
    qgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkkqvk
    pkawlsrgpsplllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwylratld
    vaaglscrvkhsslegqdivlyw
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >6v7zD (D:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7zD (D:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptedeyacrvnhvtlsqpkivkwdr
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >6v7zE (E:)
    qvqlvesggglvqaggslrlscaasgsifsinamgwyrqapgkqrdflavisssgstnya
    dsvkgrftisrdnakntaylqmnslkvedtavyycaahvagfdeynywgqgtqvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7zE (E:)
    qvqlvesggglvqaggslrlscaasgsifsinamgwyrqapgkqrdflavisssgstnya
    dsvkgrftisrdnakntaylqmnslkvedtavyycaahvagfdeynywgqgtqvtvs
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6v7zF (F:)
    qvqlvesggglvqaggslrlscaasgsifsinamgwyrqapgkqrdflavisssgstnya
    dsvkgrftisrdnakntaylqmnslkvedtavyycaahvagfdeynywgqgtqvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7zF (F:)
    qvqlvesggglvqaggslrlscaasgsifsinamgwyrqapgkqrdflavisssgstnya
    dsvkgrftisrdnakntaylqmnslkvedtavyycaahvagfdeynywgqgtqvtvs