PDB entry 2ipk

View 2ipk on RCSB PDB site
Description: Crystal Structure of the MHC Class II Molecule HLA-DR1 in Complex with the Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine) and the Superantigen, SEC3 Variant 3B2
Class: immune system
Keywords: HLA, DR1, MHC, Major Histocompatibility Complex, Fluorogenic Probe, SEC3, 4-(N,N-dimethylamino)phthalimidoalanyl, DAPA
Deposited on 2006-10-12, released 2007-03-13
The last revision prior to the SCOP 1.75 freeze date was dated 2007-04-03, with a file datestamp of 2007-06-28.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.203
AEROSPACI score: 0.48 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: hla class II histocompatibility antigen, dr alpha chain
    Species: HOMO SAPIENS
    Gene: HLA-DRA
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2ipka1, d2ipka2
  • Chain 'B':
    Compound: HLA class II histocompatibility antigen, DRB1-1 beta chain
    Species: HOMO SAPIENS
    Gene: HLA-DRB1
    Database cross-references and differences (RAF-indexed): Domains in SCOP 1.75: d2ipkb1, d2ipkb2
  • Chain 'C':
    Compound: HA related Fluorogenic Peptide, AcPKXVKQNTLKLAT (X=3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine)
    Species: synthetic, synthetic
  • Chain 'D':
    Compound: Enterotoxin type C-3
    Species: Staphylococcus aureus
    Gene: entC3
    Database cross-references and differences (RAF-indexed):
    • Uniprot P0A0L3 (1-239)
      • engineered (43)
      • engineered (45-47)
    Domains in SCOP 1.75: d2ipkd1, d2ipkd2
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2ipkA (A:)
    mikeehviiqaefylnpdqsgefmfdfdgdeifhvdmakketvwrleefgrfasfeaqga
    laniavdkanleimtkrsnytpitnvppevtvltnspvelrepnvlicfidkftppvvnv
    twlrngkpvttgvsetvflpredhlfrkfhylpflpstedvydcrvehwgldepllkhwe
    fda
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ipkA (A:)
    eehviiqaefylnpdqsgefmfdfdgdeifhvdmakketvwrleefgrfasfeaqgalan
    iavdkanleimtkrsnytpitnvppevtvltnspvelrepnvlicfidkftppvvnvtwl
    rngkpvttgvsetvflpredhlfrkfhylpflpstedvydcrvehwgldepllkhwefd
    

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2ipkB (B:)
    gdtrprflwqlkfechffngtervrllerciynqeesvrfdsdvgeyravtelgrpdaey
    wnsqkdlleqrraavdtycrhnygvgesftvqrrvepkvtvypsktqplqhhnllvcsvs
    gfypgsievrwfrngqeekagvvstgliqngdwtfqtlvmletvprsgevytcqvehpsv
    tspltvewra
    

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2ipkD (D:)
    mesqpdpmpddlhksseftgtmgnmkylyddhyvsatkvksvdsffkwdliynisdkklk
    nydkvktellnedlakkykdevvdvygsnyyvncyfsskdnvgkvtggktcmyggitkhe
    gnhfdngnlqnvlvrvyenkrntisfevqtdkksvtaqeldikarnflinkknlyefnss
    pyetgyikfienngntfwydmmpapgdkfdqskylmmyndnktvdsksvkievhlttkng
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ipkD (D:)
    esqpdpmpddlhksseftgtmgnmkylyddhyvsatkvksvdsffkwdliynisdkklkn
    ydkvktellnedlakkykdevvdvygsnyyvncyfsskggktcmyggitkhegnhfdngn
    lqnvlvrvyenkrntisfevqtdkksvtaqeldikarnflinkknlyefnsspyetgyik
    fienngntfwydmmpapgdkfdqskylmmyndnktvdsksvkievhlttkng