PDB entry 4l8d

View 4l8d on RCSB PDB site
Description: Crystal structure of the H2Db in complex with the NP-N5D peptide
Class: immune system
Keywords: Influenza, viral escape, T cell immunity, IMMUNE SYSTEM
Deposited on 2013-06-16, released 2013-10-16
The last revision prior to the SCOPe 2.03 freeze date was dated 2013-12-04, with a file datestamp of 2013-11-29.
Experiment type: XRAY
Resolution: 1.9 Å
R-factor: 0.19
AEROSPACI score: 0.4 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: H-2 class I histocompatibility antigen, D-B alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d4l8da1, d4l8da2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (Start-98)
      • see remark 999 (84)
    Domains in SCOPe 2.03: d4l8db_
  • Chain 'C':
    Compound: H-2 class I histocompatibility antigen, D-B alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.03: d4l8dc1, d4l8dc2
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (Start-98)
      • see remark 999 (84)
    Domains in SCOPe 2.03: d4l8dd_
  • Chain 'E':
    Compound: NP-N5D peptide
    Database cross-references and differences (RAF-indexed):
    • PDB 4L8D (0-8)
  • Chain 'F':
    Compound: NP-N5D peptide
    Database cross-references and differences (RAF-indexed):
    • PDB 4L8D (0-8)
  • Heterogens: SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >4l8dA (A:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
    rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
    fqkwasvvvplgkeqnytcrvyheglpepltlrwepppst
    

    Sequence, based on observed residues (ATOM records): (download)
    >4l8dA (A:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
    rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
    fqkwasvvvplgkeqnytcrvyheglpepltlrwepp
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >4l8dB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhdsmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4l8dB (B:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhdsmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >4l8dC (C:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
    rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
    fqkwasvvvplgkeqnytcrvyheglpepltlrwepppst
    

    Sequence, based on observed residues (ATOM records): (download)
    >4l8dC (C:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
    rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
    fqkwasvvvplgkeqnytcrvyheglpepltlrwepp
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >4l8dD (D:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhdsmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >4l8dD (D:)
    qktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdws
    fyilahteftptetdtyacrvkhdsmaepktvywdrdm
    

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.