PDB entry 2ybr

View 2ybr on RCSB PDB site
Description: crystal structure of the human derived single chain antibody fragment (scfv) 9004g in complex with cn2 toxin from the scorpion centruroides noxius hoffmann
Class: immune system/toxin
Keywords: immune system-toxin complex, scorpion toxin
Deposited on 2011-03-09, released 2011-04-13
The last revision prior to the SCOPe 2.06 freeze date was dated 2011-06-15, with a file datestamp of 2011-06-10.
Experiment type: XRAY
Resolution: 2.55 Å
R-factor: 0.19455
AEROSPACI score: 0.32 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: single chain antibody fragment 9004g
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 2YBR (Start-116)
    Domains in SCOPe 2.06: d2ybra_
  • Chain 'B':
    Compound: single chain antibody fragment 9004g
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 2YBR
    Domains in SCOPe 2.06: d2ybrb_
  • Chain 'C':
    Compound: beta-mammal toxin cn2
    Species: CENTRUROIDES NOXIUS HOFFMANN [TaxId:6878]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2ybrc_
  • Chain 'D':
    Compound: single chain antibody fragment 9004g
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 2YBR (0-End)
    Domains in SCOPe 2.06: d2ybrd_
  • Chain 'E':
    Compound: single chain antibody fragment 9004g
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 2YBR
    Domains in SCOPe 2.06: d2ybre_
  • Chain 'F':
    Compound: beta-mammal toxin cn2
    Species: CENTRUROIDES NOXIUS HOFFMANN [TaxId:6878]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2ybrf_
  • Chain 'G':
    Compound: single chain antibody fragment 9004g
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 2YBR (0-End)
    Domains in SCOPe 2.06: d2ybrg_
  • Chain 'H':
    Compound: single chain antibody fragment 9004g
    Species: Homo sapiens [TaxId:9606]
    Gene:
    Database cross-references and differences (RAF-indexed):
    • PDB 2YBR
    Domains in SCOPe 2.06: d2ybrh_
  • Chain 'I':
    Compound: beta-mammal toxin cn2
    Species: CENTRUROIDES NOXIUS HOFFMANN [TaxId:6878]
    Gene:
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d2ybri_
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2ybrA (A:)
    evqlvesggglvqpggslrlsctgsgftfdnyamhwlrqvpgeglewvsgisrssgdidy
    adsvkgrftisrddakktlslqmnslraedtavyycarggvgsfdtwgqgtmvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrA (A:)
    vqlvesggglvqpggslrlsctgsgftfdnyamhwlrqvpgeglewvsgisrssgdidya
    dsvkgrftisrddakktlslqmnslraedtavyycarggvgsfdtwgqgtmvtvss
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2ybrB (B:)
    ggggsggggsggggseivltqspatlsvspgeratlscrasqsvrsylawyqqkpgqapr
    llfsdasnratgiparftgsgsgtdftltisslepedfaiyycqqyrysprtfgqgtkve
    ikraaaeqkliseedlngaahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrB (B:)
    ggggseivltqspatlsvspgeratlscrasqsvrsylawyqqkpgqaprllfsdasnra
    tgiparftgsgsgtdftltisslepedfaiyycqqyrysprtfgqgtkveik
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2ybrC (C:)
    kegylvdkntgckyeclklgdndyclreckqqygkgaggycyafacwcthlyeqaivwpl
    pnkrcs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrC (C:)
    kegylvdkntgckyeclklgdndyclreckqqygkgaggycyafacwcthlyeqaivwpl
    pnkrc
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2ybrD (D:)
    evqlvesggglvqpggslrlsctgsgftfdnyamhwlrqvpgeglewvsgisrssgdidy
    adsvkgrftisrddakktlslqmnslraedtavyycarggvgsfdtwgqgtmvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrD (D:)
    evqlvesggglvqpggslrlsctgsgftfdnyamhwlrqvpgeglewvsgisrssgdidy
    adsvkgrftisrddakktlslqmnslraedtavyycarggvgsfdtwgqgtmvtv
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >2ybrE (E:)
    ggggsggggsggggseivltqspatlsvspgeratlscrasqsvrsylawyqqkpgqapr
    llfsdasnratgiparftgsgsgtdftltisslepedfaiyycqqyrysprtfgqgtkve
    ikraaaeqkliseedlngaahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrE (E:)
    seivltqspatlsvspgeratlscrasqsvrsylawyqqkpgqaprllfsdasnratgip
    arftgsgsgtdftltisslepedfaiyycqqyrysprtfgqgtkvei
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >2ybrF (F:)
    kegylvdkntgckyeclklgdndyclreckqqygkgaggycyafacwcthlyeqaivwpl
    pnkrcs
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrF (F:)
    kegylvdkntgckyeclklgdndyclreckqqygkgaggycyafacwcthlyeqaivwpl
    pnkrc
    

  • Chain 'G':
    Sequence, based on SEQRES records: (download)
    >2ybrG (G:)
    evqlvesggglvqpggslrlsctgsgftfdnyamhwlrqvpgeglewvsgisrssgdidy
    adsvkgrftisrddakktlslqmnslraedtavyycarggvgsfdtwgqgtmvtvss
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrG (G:)
    evqlvesggglvqpggslrlsctgsgftfdnyamhwlrqvpgeglewvsgisrssgdidy
    adsvkgrftisrddakktlslqmnslraedtavyycarggvgsfdtwgqgtmvtv
    

  • Chain 'H':
    Sequence, based on SEQRES records: (download)
    >2ybrH (H:)
    ggggsggggsggggseivltqspatlsvspgeratlscrasqsvrsylawyqqkpgqapr
    llfsdasnratgiparftgsgsgtdftltisslepedfaiyycqqyrysprtfgqgtkve
    ikraaaeqkliseedlngaahhhhhh
    

    Sequence, based on observed residues (ATOM records): (download)
    >2ybrH (H:)
    sggggseivltqspatlsvspgeratlscrasqsvrsylawyqqkpgqaprllfsdasnr
    atgiparftgsgsgtdftltisslepedfaiyycqqyrysprtfgqgtkveikr
    

  • Chain 'I':
    Sequence; same for both SEQRES and ATOM records: (download)
    >2ybrI (I:)
    kegylvdkntgckyeclklgdndyclreckqqygkgaggycyafacwcthlyeqaivwpl
    pnkrcs