PDB entry 5vid

View 5vid on RCSB PDB site
Description: Receptor binding domain of BoNT/B in complex with mini-protein binder Bot.0671.2
Class: toxin
Keywords: mini-protein binder, inhibitor, TOXIN
Deposited on 2017-04-15, released 2017-09-20
The last revision prior to the SCOPe 2.06 freeze date was dated 2017-09-20, with a file datestamp of 2017-09-15.
Experiment type: XRAY
Resolution: 2.75 Å
R-factor: N/A
AEROSPACI score: 0.18 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: botulinum neurotoxin type b
    Species: Clostridium botulinum [TaxId:1491]
    Gene: botB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vida1, d5vida2
  • Chain 'B':
    Compound: botulinum neurotoxin type b
    Species: Clostridium botulinum [TaxId:1491]
    Gene: botB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vidb1, d5vidb2
  • Chain 'C':
    Compound: botulinum neurotoxin type b
    Species: Clostridium botulinum [TaxId:1491]
    Gene: botB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vidc1, d5vidc2
  • Chain 'D':
    Compound: botulinum neurotoxin type b
    Species: Clostridium botulinum [TaxId:1491]
    Gene: botB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vidd1, d5vidd2
  • Chain 'E':
    Compound: botulinum neurotoxin type b
    Species: Clostridium botulinum [TaxId:1491]
    Gene: botB
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.06: d5vide1, d5vide2
  • Chain 'F':
    Compound: Bot.0671.2
    Species: unidentified [TaxId:32644]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VID
  • Chain 'G':
    Compound: Bot.0671.2
    Species: unidentified [TaxId:32644]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VID
  • Chain 'H':
    Compound: Bot.0671.2
    Species: unidentified [TaxId:32644]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VID
  • Chain 'I':
    Compound: Bot.0671.2
    Species: unidentified [TaxId:32644]
    Database cross-references and differences (RAF-indexed):
    • PDB 5VID
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >5vidA (A:)
    gplgseilnniilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtq
    nqniifnsvfldfsvsfwiripkykndgiqnyihneytiincmknnsgwkisirgnriiw
    tlidingktksvffeynirediseyinrwffvtitnnlnnakiyingklesntdikdire
    viangeiifkldgdidrtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplm
    ynkeyymfnagnknsyiklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksns
    qsinddivrkedyiyldffnlnqewrvytykyfkkeeeklflapisdsdefyntiqikey
    deqptyscqllfkkdeestdeigligihrfyesgivfeeykdyfciskwylkevkrkpyn
    lklgcnwqfipkdegwte
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vidA (A:)
    niilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtqsvfldfsvs
    fwiripkykndgiqnyihneytiincmknnsgwkisirgnriiwtlidingktksvffey
    nirediseyinrwffvtitnnlnnakiyingklesntdikdireviangeiifkldgdid
    rtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplmynkeyymfnagnknsy
    iklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksdivrkedyiyldffnlnq
    ewrvytykyfkkeeeklflapisdsdefyntiqikeydeqptyscqllfkkdeestdeig
    ligihrfyesgivfeeykdyfciskwylkevkrkpynlklgcnwqfipkdegwte
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >5vidB (B:)
    gplgseilnniilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtq
    nqniifnsvfldfsvsfwiripkykndgiqnyihneytiincmknnsgwkisirgnriiw
    tlidingktksvffeynirediseyinrwffvtitnnlnnakiyingklesntdikdire
    viangeiifkldgdidrtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplm
    ynkeyymfnagnknsyiklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksns
    qsinddivrkedyiyldffnlnqewrvytykyfkkeeeklflapisdsdefyntiqikey
    deqptyscqllfkkdeestdeigligihrfyesgivfeeykdyfciskwylkevkrkpyn
    lklgcnwqfipkdegwte
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vidB (B:)
    nniilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtqnldfsvsf
    wiripkykndgiqnyihneytiincmknnsgwkisirgnriiwtlidingktksvffeyn
    irediseyinrwffvtitnnlnnakiyingklesntdikdireviangeiifkldgdidr
    tqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplmynkeyymfnagnknsyi
    klkkdspvgeiltrskynqnskyinyrdlyigekfiirrkssinddivrkedyiyldffn
    lnqewrvytykyfkkeeeklflapisdsdefyntiqikeydeqptyscqllfkkdeestd
    eigligihrfyeeykdyfciskwylkevkrkpynlklgcnwqfipkdegwte
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >5vidC (C:)
    gplgseilnniilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtq
    nqniifnsvfldfsvsfwiripkykndgiqnyihneytiincmknnsgwkisirgnriiw
    tlidingktksvffeynirediseyinrwffvtitnnlnnakiyingklesntdikdire
    viangeiifkldgdidrtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplm
    ynkeyymfnagnknsyiklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksns
    qsinddivrkedyiyldffnlnqewrvytykyfkkeeeklflapisdsdefyntiqikey
    deqptyscqllfkkdeestdeigligihrfyesgivfeeykdyfciskwylkevkrkpyn
    lklgcnwqfipkdegwte
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vidC (C:)
    nniilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtqnqniisvf
    ldfsvsfwiripkykndgiqnyihneytiincmknnsgwkisirgnriiwtlidingktk
    svffeynirediseyinrwffvtitnnlnnakiyingklesntdikdireviangeiifk
    ldgdidrtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplmynkeyymfna
    gnknsyiklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksqsinddivrked
    yiyldffnlnqewrvytykyfkkeeeklflapisdsdefyntiqikeydeqptyscqllf
    kkdeestdeigligihrfyesgivfeeykdyfciskwylkevkrkpynlklgcnwqfipk
    degwte
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >5vidD (D:)
    gplgseilnniilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtq
    nqniifnsvfldfsvsfwiripkykndgiqnyihneytiincmknnsgwkisirgnriiw
    tlidingktksvffeynirediseyinrwffvtitnnlnnakiyingklesntdikdire
    viangeiifkldgdidrtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplm
    ynkeyymfnagnknsyiklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksns
    qsinddivrkedyiyldffnlnqewrvytykyfkkeeeklflapisdsdefyntiqikey
    deqptyscqllfkkdeestdeigligihrfyesgivfeeykdyfciskwylkevkrkpyn
    lklgcnwqfipkdegwte
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vidD (D:)
    niilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtqnvfldfsvs
    fwiripkykndgiqnyihneytiincmknnsgwkisirgnriiwtlidingktksvffey
    nirediseyinrwffvtitnnlnnakiyingklesntdikdireviangeiifkldgdid
    rtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplmynkeyymfnagnknsy
    iklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksnsinddivrkedyiyldf
    fnlnqewrvytykyfkkeeeklflapisdsdefyntiqikeydeqptyscqllfkkdees
    tdeigligihrfyesgivfeeykdyfciskwylkevkrkpynlklgcnwqfipkdegwte
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >5vidE (E:)
    gplgseilnniilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtq
    nqniifnsvfldfsvsfwiripkykndgiqnyihneytiincmknnsgwkisirgnriiw
    tlidingktksvffeynirediseyinrwffvtitnnlnnakiyingklesntdikdire
    viangeiifkldgdidrtqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplm
    ynkeyymfnagnknsyiklkkdspvgeiltrskynqnskyinyrdlyigekfiirrksns
    qsinddivrkedyiyldffnlnqewrvytykyfkkeeeklflapisdsdefyntiqikey
    deqptyscqllfkkdeestdeigligihrfyesgivfeeykdyfciskwylkevkrkpyn
    lklgcnwqfipkdegwte
    

    Sequence, based on observed residues (ATOM records): (download)
    >5vidE (E:)
    niilnlrykdnnlidlsgygakvevydgvelndknqfkltssanskirvtqvfldfsvsf
    wiripkykndgiqnyihneytiincmknnsgwkisirgnriiwtlidingktksvffeyn
    irediseyinrwffvtitnnlnnakiyingklesntdikdireviangeiifkldgdidr
    tqfiwmkyfsifntelsqsnieerykiqsyseylkdfwgnplmynkeyymfnagnknsyi
    klkkdspvgeiltrskynqnskyinyrdlyigekfiirrdivrkedyiyldffnlnqewr
    vytykyfkkeeeklflapisdsdefyntiqikeydeqptyscqllfkeigligihrfyes
    givfeeykdyfciskwylkevkrkpynlklgcnwqfipkdegwte
    

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.