PDB entry 5mzm

View 5mzm on RCSB PDB site
Description: Structure of H-2Db in complex with TEIPP APL Trh4 p3P
Class: immune system
Keywords: cancer, neo-epitope, T-cell epitopes associated with impaired peptide processing, MHC-I, immune system
Deposited on 2017-02-01, released 2018-03-21
The last revision prior to the SCOPe 2.07 freeze date was dated 2018-03-21, with a file datestamp of 2018-03-16.
Experiment type: XRAY
Resolution: 2.4 Å
R-factor: N/A
AEROSPACI score: 0.23 (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 2.07: d5mzma1, d5mzma2
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (0-98)
      • conflict (84)
    Domains in SCOPe 2.07: d5mzmb_
  • Chain 'C':
    Compound: Ceramide synthase 5 derived peptide Trh4 p3P
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5MZM (0-8)
  • Chain 'D':
    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 2.07: d5mzmd1, d5mzmd2
  • Chain 'E':
    Compound: Beta-2-microglobulin
    Species: Mus musculus [TaxId:10090]
    Gene: B2M
    Database cross-references and differences (RAF-indexed):
    • Uniprot P01887 (0-98)
      • conflict (84)
    Domains in SCOPe 2.07: d5mzme_
  • Chain 'F':
    Compound: Ceramide synthase 5 derived peptide Trh4 p3P
    Species: Mus musculus [TaxId:10090]
    Database cross-references and differences (RAF-indexed):
    • PDB 5MZM (0-8)
  • Heterogens: GOL, SO4, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5mzmA (A:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
    rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
    fqkwasvvvplgkeqnytcrvyheglpepltlrwep
    

    Sequence, based on observed residues (ATOM records): (download)
    >5mzmA (A:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnrtds
    pkahvthhprkgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgtfqkwa
    svvvplgkeqnytcrvyheglpepltlrwep
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5mzmB (B:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhdsmaepktvywdrdm
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5mzmD (D:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylkngnatll
    rtdspkahvthhprskgevtlrcwalgfypaditltwqlngeeltqdmelvetrpagdgt
    fqkwasvvvplgkeqnytcrvyheglpepltlrwep
    

    Sequence, based on observed residues (ATOM records): (download)
    >5mzmD (D:)
    gphsmryfetavsrpgleepryisvgyvdnkefvrfdsdaenpryeprapwmeqegpeyw
    eretqkakgqeqwfrvslrnllgyynqsaggshtlqqmsgcdlgsdwrllrgylqfayeg
    rdyialnedlktwtaadmaaqitrrkweqsgaaehykaylegecvewlhrylknglrtds
    pkahvthhprskgevtlrcwalgfypaditltwqlngeetqdmelvetrpagdgtfqkwa
    svvvplgkeqnytcrvyheglpepltlrwep
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records: (download)
    >5mzmE (E:)
    iqktpqiqvysrhppengkpnilncyvtqfhpphieiqmlkngkkipkvemsdmsfskdw
    sfyilahteftptetdtyacrvkhdsmaepktvywdrdm
    

  • Chain 'F':
    No sequence available.