PDB entry 5hgd

View 5hgd on RCSB PDB site
Description: hla*a2402 complexed with hiv nef138 y2f mutant 10mer epitope
Deposited on 2016-01-08, released 2016-06-08
The last revision was dated 2019-12-18, with a file datestamp of 2019-12-13.
Experiment type: XRAY
Resolution: 2.07 Å
R-factor: N/A
AEROSPACI score: 0.3 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: HLA class I histocompatibility antigen, A-24 alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: HLA-A, HLAA
    Database cross-references and differences (RAF-indexed):
  • Chain 'B':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61769 (1-99)
      • initiating methionine (0)
  • Chain 'C':
    Compound: Protein Nef
    Species: Human immunodeficiency virus type 1, synthetic [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18801 (0-9)
      • engineered mutation (1)
  • Chain 'D':
    Compound: HLA class I histocompatibility antigen, A-24 alpha chain
    Species: Homo sapiens [TaxId:9606]
    Gene: HLA-A, HLAA
    Database cross-references and differences (RAF-indexed):
  • Chain 'E':
    Compound: Beta-2-microglobulin
    Species: Homo sapiens [TaxId:9606]
    Gene: B2M, CDABP0092, HDCMA22P
    Database cross-references and differences (RAF-indexed):
    • Uniprot P61769 (1-99)
      • initiating methionine (0)
  • Chain 'F':
    Compound: Protein Nef
    Species: Human immunodeficiency virus type 1, synthetic [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P18801 (0-9)
      • engineered mutation (1)
  • Heterogens: HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.07, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >5hgdA (A:)
    mgshsmryfstsvsrpgrgeprfiavgyvddtqfvrfdsdaasqrmeprapwieqegpey
    wdeetgkvkahsqtdrenlrialryynqseagshtlqmmfgcdvgsdgrflrgyhqyayd
    gkdyialkedlrswtaadmaaqitkrkweaahvaeqqraylegtcvdglrrylengketl
    qrtdppkthmthhpisdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdg
    tfqkwaavvvpsgeeqrytchvqheglpkpltlrw
    

    Sequence, based on observed residues (ATOM records):
    >5hgdA (A:)
    gshsmryfstsvsrpgrgeprfiavgyvddtqfvrfdsdaasqrmeprapwieqegpeyw
    deetgkvkahsqtdrenlrialryynqseagshtlqmmfgcdvgsdgrflrgyhqyaydg
    kdyialkedlrswtaadmaaqitkrkweaahvaeqqraylegtcvdglrrylengketlq
    rtdppkthmthhpisdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdgt
    fqkwaavvvpsgeeqrytchvqheglpkpltlrw
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records:
    >5hgdB (B:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >5hgdC (C:)
    rfpltfgwcf
    

  • Chain 'D':
    Sequence, based on SEQRES records:
    >5hgdD (D:)
    mgshsmryfstsvsrpgrgeprfiavgyvddtqfvrfdsdaasqrmeprapwieqegpey
    wdeetgkvkahsqtdrenlrialryynqseagshtlqmmfgcdvgsdgrflrgyhqyayd
    gkdyialkedlrswtaadmaaqitkrkweaahvaeqqraylegtcvdglrrylengketl
    qrtdppkthmthhpisdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdg
    tfqkwaavvvpsgeeqrytchvqheglpkpltlrw
    

    Sequence, based on observed residues (ATOM records):
    >5hgdD (D:)
    gshsmryfstsvsrpgrgeprfiavgyvddtqfvrfdsdaasqrmeprapwieqegpeyw
    deetgkvkahsqtdrenlrialryynqseagshtlqmmfgcdvgsdgrflrgyhqyaydg
    kdyialkedlrswtaadmaaqitkrkweaahvaeqqraylegtcvdglrrylengketlq
    rtdppkthmthhpisdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdgt
    fqkwaavvvpsgeeqrytchvqheglpkpltlrw
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >5hgdE (E:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >5hgdF (F:)
    rfpltfgwcf