PDB entry 3nfj

View 3nfj on RCSB PDB site
Description: Recognition of peptide-MHC by a V-delta/V-beta TCR
Deposited on 2010-06-10, released 2011-06-29
The last revision was dated 2011-07-13, with a file datestamp of 2011-07-08.
Experiment type: XRAY
Resolution: 2.68 Å
R-factor: 0.205
AEROSPACI score: 0.29 (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: 10-mer peptide from Protein Nef
    Species: Human immunodeficiency virus 1, synthetic [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • 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: 10-mer peptide from Protein Nef
    Species: Human immunodeficiency virus 1, synthetic [TaxId:11676]
    Database cross-references and differences (RAF-indexed):
  • Chain 'G':
    Compound: T cell receptor V-delta+C-alpha chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3NFJ
  • Chain 'H':
    Compound: T cell receptor beta chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3NFJ (0-244)
  • Chain 'I':
    Compound: T cell receptor V-delta+C-alpha chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3NFJ
  • Chain 'J':
    Compound: T cell receptor beta chain
    Species: Homo sapiens [TaxId:9606]
    Database cross-references and differences (RAF-indexed):
    • PDB 3NFJ (0-244)
  • 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; same for both SEQRES and ATOM records:
    >3nfjA (A:)
    gshsmryfstsvsrpgrgeprfiavgyvddtqfvrfdsdaasqrmeprapwieqegpeyw
    deetgkvkahsqtdrenlrialryynqseagshtlqmmfgcdvgsdgrflrgyhqyaydg
    kdyialkedlrswtaadmaaqitkrkweaahvaeqqraylegtcvdglrrylengketlq
    rtdppkthmthhpisdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdgt
    fqkwaavvvpsgeeqrytchvqheglpkpltlrw
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records:
    >3nfjB (B:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records:
    >3nfjC (C:)
    rypltfgwcf
    

  • Chain 'D':
    Sequence; same for both SEQRES and ATOM records:
    >3nfjD (D:)
    gshsmryfstsvsrpgrgeprfiavgyvddtqfvrfdsdaasqrmeprapwieqegpeyw
    deetgkvkahsqtdrenlrialryynqseagshtlqmmfgcdvgsdgrflrgyhqyaydg
    kdyialkedlrswtaadmaaqitkrkweaahvaeqqraylegtcvdglrrylengketlq
    rtdppkthmthhpisdheatlrcwalgfypaeitltwqrdgedqtqdtelvetrpagdgt
    fqkwaavvvpsgeeqrytchvqheglpkpltlrw
    

  • Chain 'E':
    Sequence; same for both SEQRES and ATOM records:
    >3nfjE (E:)
    miqrtpkiqvysrhpaengksnflncyvsgfhpsdievdllkngeriekvehsdlsfskd
    wsfyllyyteftptekdeyacrvnhvtlsqpkivkwdrdm
    

  • Chain 'F':
    Sequence; same for both SEQRES and ATOM records:
    >3nfjF (F:)
    rypltfgwcf
    

  • Chain 'G':
    Sequence, based on SEQRES records:
    >3nfjG (G:)
    aqkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaks
    grysvnfkkaaksvaltisalqledsakyfcalgelarsggyqkvtfgtgtklqvipniq
    npdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsav
    awsnksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records):
    >3nfjG (G:)
    qkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaksg
    rysvnfkkaaksvaltisalqledsakyfcalgelarsggyqkvtfgtgtklqvipniqn
    pdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsava
    wsnksdfacanafnnsiipedtffpsp
    

  • Chain 'H':
    Sequence; same for both SEQRES and ATOM records:
    >3nfjH (H:)
    sqtihqwpatlvqpvgsplslectvegtsnpnlywyrqaagrglqllfysvgigqissev
    pqnlsasrpqdrqfilsskklllsdsgfylcawsvsvgagvptiyfgegswltvvedlnk
    vfppevavfepseaeishtqkatlvclatgffpdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad
    

  • Chain 'I':
    Sequence, based on SEQRES records:
    >3nfjI (I:)
    aqkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaks
    grysvnfkkaaksvaltisalqledsakyfcalgelarsggyqkvtfgtgtklqvipniq
    npdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsav
    awsnksdfacanafnnsiipedtffpspess
    

    Sequence, based on observed residues (ATOM records):
    >3nfjI (I:)
    qkvtqaqssvsmpvrkavtlnclyetswwsyyifwykqlpskemiflirqgsdeqnaksg
    rysvnfkkaaksvaltisalqledsakyfcalgelarsggyqkvtfgtgtklqvipniqn
    pdpavyqlrdskssdksvclftdfdsqtnvsqskdsdvyitdkcvldmrsmdfksnsava
    wsnksdfacanafnnsiipedtffpsp
    

  • Chain 'J':
    Sequence; same for both SEQRES and ATOM records:
    >3nfjJ (J:)
    sqtihqwpatlvqpvgsplslectvegtsnpnlywyrqaagrglqllfysvgigqissev
    pqnlsasrpqdrqfilsskklllsdsgfylcawsvsvgagvptiyfgegswltvvedlnk
    vfppevavfepseaeishtqkatlvclatgffpdhvelswwvngkevhsgvctdpqplke
    qpalndsryalssrlrvsatfwqnprnhfrcqvqfyglsendewtqdrakpvtqivsaea
    wgrad