PDB entry 3u0p

View 3u0p on RCSB PDB site
Description: Crystal structure of human CD1d-lysophosphatidylcholine
Class: immune system
Keywords: Antigen presentation, Natura Killer T cell receptor, Cell surface, IMMUNE SYSTEM
Deposited on 2011-09-28, released 2012-04-25
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-11-08, with a file datestamp of 2017-11-03.
Experiment type: XRAY
Resolution: 2.8 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 CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-277)
      • engineered mutation (42)
      • engineered mutation (108)
      • engineered mutation (163)
      • expression tag (278)
    Domains in SCOPe 2.07: d3u0pa1, d3u0pa2, d3u0pa3
  • Chain 'B':
    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: d3u0pb_
  • Chain 'C':
    Compound: Antigen-presenting glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-277)
      • engineered mutation (42)
      • engineered mutation (108)
      • engineered mutation (163)
      • expression tag (278-279)
    Domains in SCOPe 2.07: d3u0pc1, d3u0pc2, d3u0pc3
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61769 (3-101)
      • expression tag (2)
    Domains in SCOPe 2.07: d3u0pd1, d3u0pd2
  • Chain 'E':
    Compound: Antigen-presenting glycoprotein CD1d
    Species: Homo sapiens [TaxId:9606]
    Gene: CD1D
    Database cross-references and differences (RAF-indexed):
    • Uniprot P15813 (Start-277)
      • engineered mutation (42)
      • engineered mutation (163)
    Domains in SCOPe 2.07: d3u0pe1, d3u0pe2
  • Chain 'F':
    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: d3u0pf_
  • Heterogens: NAG, FUC, LSC, HEX, SO4, GOL, UND, NBU, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >3u0pA (A:)
    adpvpqrlfplrclqissfansswtrtdglawlgelqthswsqdsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgqasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllqgtcpqfvsgllesgks
    elkkqvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpna
    detwylratldvvageaaglscrvkhsslegqdivlywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u0pA (A:)
    rlfplrclqissfansswtrtdglawlgelqthswsqdsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgqasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllqgtcpqfvsgllesgkselkkqv
    kpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwyl
    ratldvvageaaglscrvkhsslegqdivlywh
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >3u0pB (B:)
    adpiqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfs
    kdwsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u0pB (B:)
    iqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskdw
    sfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >3u0pC (C:)
    adpvpqrlfplrclqissfansswtrtdglawlgelqthswsqdsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgqasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllqgtcpqfvsgllesgks
    elkkqvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpna
    detwylratldvvageaaglscrvkhsslegqdivlywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u0pC (C:)
    rlfplrclqissfansswtrtdglawlgelqthswsqdsdtvrslkpwsqgtfsdqqwet
    lqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgqasnnffhvafqgkdils
    fqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllqgtcpqfvsgllesgkselkkqv
    kpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpnadetwyl
    ratldvvageaaglscrvkhsslegqdivlywhh
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >3u0pD (D:)
    adpiqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfs
    kdwsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u0pD (D:)
    piqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >3u0pE (E:)
    adpvpqrlfplrclqissfansswtrtdglawlgelqthswsqdsdtvrslkpwsqgtfs
    dqqwetlqhifrvyrssftrdvkefakmlrlsyplelqvsagcevhpgqasnnffhvafq
    gkdilsfqgtsweptqeaplwvnlaiqvlnqdkwtretvqwllqgtcpqfvsgllesgks
    elkkqvkpkawlsrgpspgpgrlllvchvsgfypkpvwvkwmrgeqeqqgtqpgdilpna
    detwylratldvvageaaglscrvkhsslegqdivlywhhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u0pE (E:)
    lfplrclqissfansswtrtdglawlgelqthswsqdsdtvrslkpwsqgtfsdqwetlq
    hifrvyrssftrdvkefakmlrlsyplelqvsagcevhsnnffhvafqgkdilsfqgtsw
    eptqeaplwvnlaiqvlnqdkwtretvqwllqgtcpqfvsgllesgkselkkqvkpkawl
    srlllvchvsgfypkpvwvpgdilpnadetwylrvkhssleqdivlyw
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >3u0pF (F:)
    adpiqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfs
    kdwsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >3u0pF (F:)
    qrtpkiqvysrhpangsnflncyvsgfhpsdivdlneriekvehsdlsfskdwsfyllyy
    ftptekcrvhvtlsqpkivkwd