PDB entry 6v7y

View 6v7y on RCSB PDB site
Description: Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5
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: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.28 (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-End)
      • initiating methionine (0)
    • PDB 6V7Y
    Domains in SCOPe 2.07: d6v7ya1, d6v7ya2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61769 (1-99)
      • initiating methionine (0)
    Domains in SCOPe 2.07: d6v7yb1, d6v7yb2
  • Chain 'F':
    Compound: Nanobody VHH ID5
    Species: LAMA GLAMA [TaxId:9844]
    Database cross-references and differences (RAF-indexed):
    • PDB 6V7Y (Start-126)
    Domains in SCOPe 2.07: d6v7yf_
  • Heterogens: AGH, NAG, SO4, CL, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >6v7yA (A:)
    mqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqw
    etlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdi
    lsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkk
    qvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetw
    ylratldvvageaaglscrvkhsslegqdivlywgslvprgsgsriarleekvktlkaqn
    selastanmlreqvaqlkqkvmnhgsglndifeaqkiewhehhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7yA (A:)
    mqrlfplrclqissfansswtrtdglawlgelqthswsndsdtvrslkpwsqgtfsdqqw
    etlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgnasnnffhvafqgkdi
    lsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllngtcpqfvsgllesgkselkk
    qvkpkawlsrgpspgrlllvchvsgfypkpvwvkwmreqeqqgtqpgdilpnadetwylr
    atldvvagaaglscrvkhsslegqdivlyw
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >6v7yB (B:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >6v7yF (F:)
    evqlvesggglvqaggslrlscaasgssfssytmgwfrqapgkereivagirwsdespiy
    adsvkgrftisrdnakntlylqmnslkpedtavyycaarlvppgipiprtsesmrywgkg
    tlvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >6v7yF (F:)
    vqlvesggglvqaggslrlscaasgssfssytmgwfrqapgkereivagirwsdespiya
    dsvkgrftisrdnakntlylqmnslkpedtavyycaarlvppgipiprtsesmrywgkgt
    lvtvss