PDB entry 6hby

View 6hby on RCSB PDB site
Description: hla class ii peptide flanking residues tune the immunogenicity of a human tumor-derived epitope
Deposited on 2018-08-13, released 2019-08-14
The last revision was dated 2020-01-29, with a file datestamp of 2020-01-24.
Experiment type: XRAY
Resolution: 1.95 Å
R-factor: N/A
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: hla class II histocompatibility antigen, dr alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: HLA-DRA, HLA-DRA1
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: HLA class II histocompatibility antigen, DRB1-1 beta chain
    Species: Homo sapiens [TaxId:9606]
    Gene: HLA-DRB1
    Database cross-references and differences (RAF-indexed):
    • Uniprot P04229 (1-190)
      • initiating methionine (0)
  • Chain 'C':
    Compound: ARRPPLAELAALNLSGSRL 5T4 tumour epitope
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6HBY (0-18)
  • Chain 'D':
    Compound: hla class II histocompatibility antigen, dr alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: HLA-DRA, HLA-DRA1
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: HLA class II histocompatibility antigen, DRB1-1 beta chain
    Species: Homo sapiens [TaxId:9606]
    Gene: HLA-DRB1
    Database cross-references and differences (RAF-indexed):
  • Chain 'F':
    Compound: ARRPPLAELAALNLSGSRL 5T4 tumour epitope
    Species: HOMO SAPIENS, synthetic [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 6HBY (0-18)
  • Heterogens: EDO, PO4, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence; same for both SEQRES and ATOM records:
    >6hbyA (A:)
eehviiqaefylnpdqsgefmfdfdgdeifhvdmakketvwrleefgrfasfeaqgalan
iavdkanleimtkrsnytpitnvppevtvltnspvelrepnvlicfidkftppvvnvtwl
rngkpvttgvsetvflpredhlfrkfhylpflpstedvydcrvehwgldepllkhwef

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records:
    >6hbyB (B:)
mgdtrprflwqlkfechffngtervrllerciynqeesvrfdsdvgeyravtelgrpdae
ywnsqkdlleqrraavdtycrhnygvgesftvqrrvepkvtvypsktqplqhhnllvcsv
sgfypgsievrwfrngqeekagvvstgliqngdwtfqtlvmletvprsgevytcqvehps
vtspltvewra

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >6hbyC (C:)
arrpplaelaalnlsgsrl

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >6hbyD (D:)
keehviiqaefylnpdqsgefmfdfdgdeifhvdmakketvwrleefgrfasfeaqgala
niavdkanleimtkrsnytpitnvppevtvltnspvelrepnvlicfidkftppvvnvtw
lrngkpvttgvsetvflpredhlfrkfhylpflpstedvydcrvehwgldepllkhwefd

  • Chain 'E':
    Sequence, based on SEQRES records:
    >6hbyE (E:)
mgdtrprflwqlkfechffngtervrllerciynqeesvrfdsdvgeyravtelgrpdae
ywnsqkdlleqrraavdtycrhnygvgesftvqrrvepkvtvypsktqplqhhnllvcsv
sgfypgsievrwfrngqeekagvvstgliqngdwtfqtlvmletvprsgevytcqvehps
vtspltvewra

    Sequence, based on observed residues (ATOM records):
    >6hbyE (E:)
gdtrprflwqlkfechffngtervrllerciynqeesvrfdsdvgeyravtelgrpdaey
wnsqkdlleqrraavdtycrhnygvgesftvqrrvepkvtvypsktqplqhhnllvcsvs
gfypgsievrwfrngqeekagvvstgliqngdwtfqtlvmletvprsgevytcqvehpsv
tspltvewra

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >6hbyF (F:)
arrpplaelaalnlsgsrl