PDB entry 5kd4

View 5kd4 on RCSB PDB site
Description: Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PVI10) of HIV gp120 MN Isolate (IGPGRAFYVI)
Class: immune system
Keywords: MAJOR HISTOMPATIBILITY COMPLEX CLASS I, MHC-I, H2-Dd, H-2Dd, HIV peptide, PVI10, GLYCOPROTEIN, IMMUNE RESPONSE, IMMUNE SYSTEM
Deposited on 2016-06-07, released 2017-10-11
The last revision prior to the SCOPe 2.06 freeze date was dated 2017-10-11, with a file datestamp of 2017-10-06.
Experiment type: XRAY
Resolution: 3.05 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: H-2 class I histocompatibility antigen, D-D alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5kd4a1, d5kd4a2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5kd4b_
  • Chain 'C':
    Compound: H-2 class I histocompatibility antigen, D-D alpha chain
    Species: Mus musculus [TaxId:10090]
    Gene: H2-D1
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5kd4c1, d5kd4c2
  • Chain 'D':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5kd4d_
  • Chain 'P':
    Compound: Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • PDB 5KD4 (0-9)
  • Chain 'Q':
    Compound: Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)
    Species: Human immunodeficiency virus 1 [TaxId:11676]
    Gene: ENV
    Database cross-references and differences (RAF-indexed):
    • PDB 5KD4 (0-9)

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5kd4A (A:)
    mshslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeyw
    eretrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydg
    cdyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatll
    rtdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgt
    fqkwasvvvplgkeqkytchveheglpepltlrwgke
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kd4A (A:)
    shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
    retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
    dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
    tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
    qkwasvvvplgkeqkytchveheglpepltlrw
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5kd4B (B:)
    miqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskd
    wsfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kd4B (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5kd4C (C:)
    mshslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeyw
    eretrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydg
    cdyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatll
    rtdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgt
    fqkwasvvvplgkeqkytchveheglpepltlrwgke
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kd4C (C:)
    shslryfvtavsrpgfgeprymevgyvdntefvrfdsdaenpryeprarwieqegpeywe
    retrrakgneqsfrvdlrtalryynqsaggshtlqwmagcdvesdgrllrgywqfaydgc
    dyialnedlktwtaadmaaqitrrkweqagaaerdraylegecvewlrrylkngnatllr
    tdppkahvthhrrpegdvtlrcwalgfypaditltwqlngeeltqemelvetrpagdgtf
    qkwasvvvplgkeqkytchveheglpepltlrw
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5kd4D (D:)
    miqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskd
    wsfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

    Sequence, based on observed residues (ATOM records): (download)
    >5kd4D (D:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhasmaepktvywdrdm
    

  • Chain 'P':
    No sequence available.

  • Chain 'Q':
    No sequence available.