PDB entry 1vkd

View 1vkd on RCSB PDB site
Description: Crystal structure of a predicted glycosidase (tm1225) from thermotoga maritima msb8 at 2.10 A resolution
Class: hydrolase
Keywords: Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI, hydrolase
Deposited on 2004-05-12, released 2004-05-25
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-10-04, with a file datestamp of 2017-09-29.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: N/A
AEROSPACI score: 0.28 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: conserved hypothetical protein TM1225
    Species: THERMOTOGA MARITIMA [TaxId:243274]
    Gene: TM1225
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9X0V2 (12-337)
      • leader sequence (11)
      • modified residue (12)
      • modified residue (144)
      • modified residue (178)
      • modified residue (201)
      • modified residue (337)
    Domains in SCOPe 2.07: d1vkda1, d1vkda2
  • Chain 'B':
    Compound: conserved hypothetical protein TM1225
    Species: THERMOTOGA MARITIMA [TaxId:243274]
    Gene: TM1225
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9X0V2 (12-337)
      • modified residue (12)
      • modified residue (144)
      • modified residue (178)
      • modified residue (201)
      • modified residue (337)
    Domains in SCOPe 2.07: d1vkdb_
  • Chain 'C':
    Compound: conserved hypothetical protein TM1225
    Species: THERMOTOGA MARITIMA [TaxId:243274]
    Gene: TM1225
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9X0V2 (12-337)
      • modified residue (12)
      • modified residue (144)
      • modified residue (178)
      • modified residue (201)
      • modified residue (337)
    Domains in SCOPe 2.07: d1vkdc_
  • Chain 'D':
    Compound: conserved hypothetical protein TM1225
    Species: THERMOTOGA MARITIMA [TaxId:243274]
    Gene: TM1225
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9X0V2 (12-337)
      • modified residue (12)
      • modified residue (144)
      • modified residue (178)
      • modified residue (201)
      • modified residue (337)
    Domains in SCOPe 2.07: d1vkdd_
  • Chain 'E':
    Compound: conserved hypothetical protein TM1225
    Species: THERMOTOGA MARITIMA [TaxId:243274]
    Gene: TM1225
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9X0V2 (12-End)
      • modified residue (12)
      • modified residue (144)
      • modified residue (178)
      • modified residue (201)
    Domains in SCOPe 2.07: d1vkde_
  • Chain 'F':
    Compound: conserved hypothetical protein TM1225
    Species: THERMOTOGA MARITIMA [TaxId:243274]
    Gene: TM1225
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q9X0V2 (12-337)
      • modified residue (12)
      • modified residue (144)
      • modified residue (178)
      • modified residue (201)
      • modified residue (337)
    Domains in SCOPe 2.07: d1vkdf_
  • Heterogens: TRS, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >1vkdA (A:)
    mgsdkihhhhhhmkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsa
    vvpyngefvgvfridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydpr
    vvkiedtyyitfctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvml
    nrpsdnghtpfgdiflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwll
    iyhgvtltcngyvysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaal
    cdadtgrvaiyygaadthvalafgyideivdfvkrnsm
    

    Sequence, based on observed residues (ATOM records): (download)
    >1vkdA (A:)
    hmkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsavvpyngefvgv
    fridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydprvvkiedtyyit
    fctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvmlnrpsdnghtpf
    gdiflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwlliyhgvtltcng
    yvysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaalcdadtgrvaiy
    ygaadthvalafgyideivdfvkrnsm
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >1vkdB (B:)
    mgsdkihhhhhhmkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsa
    vvpyngefvgvfridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydpr
    vvkiedtyyitfctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvml
    nrpsdnghtpfgdiflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwll
    iyhgvtltcngyvysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaal
    cdadtgrvaiyygaadthvalafgyideivdfvkrnsm
    

    Sequence, based on observed residues (ATOM records): (download)
    >1vkdB (B:)
    mkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsavvpyngefvgvf
    ridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydprvvkiedtyyitf
    ctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvmlnrpsdnghtpfg
    diflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwlliyhgvtltcngy
    vysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaalcdadtgrvaiyy
    gaadthvalafgyideivdfvkrnsm
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >1vkdC (C:)
    mgsdkihhhhhhmkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsa
    vvpyngefvgvfridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydpr
    vvkiedtyyitfctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvml
    nrpsdnghtpfgdiflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwll
    iyhgvtltcngyvysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaal
    cdadtgrvaiyygaadthvalafgyideivdfvkrnsm
    

    Sequence, based on observed residues (ATOM records): (download)
    >1vkdC (C:)
    mkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsavvpyngefvgvf
    ridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydprvvkiedtyyitf
    ctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvmlnrpsdnghtpfg
    diflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwlliyhgvtltcngy
    vysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaalcdadtgrvaiyy
    gaadthvalafgyideivdfvkrnsm
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >1vkdD (D:)
    mgsdkihhhhhhmkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsa
    vvpyngefvgvfridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydpr
    vvkiedtyyitfctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvml
    nrpsdnghtpfgdiflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwll
    iyhgvtltcngyvysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaal
    cdadtgrvaiyygaadthvalafgyideivdfvkrnsm
    

    Sequence, based on observed residues (ATOM records): (download)
    >1vkdD (D:)
    mkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsavvpyngefvgvf
    ridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydprvvkiedtyyitf
    ctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvmlnrpsdnghtpfg
    diflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwlliyhgvtltcngy
    vysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaalcdadtgrvaiyy
    gaadthvalafgyideivdfvkrnsm
    

  • Chain 'E':
    Sequence, based on SEQRES records: (download)
    >1vkdE (E:)
    mgsdkihhhhhhmkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsa
    vvpyngefvgvfridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydpr
    vvkiedtyyitfctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvml
    nrpsdnghtpfgdiflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwll
    iyhgvtltcngyvysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaal
    cdadtgrvaiyygaadthvalafgyideivdfvkrnsm
    

    Sequence, based on observed residues (ATOM records): (download)
    >1vkdE (E:)
    mkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsavvpyngefvgvf
    ridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydprvvkiedtyyitf
    ctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvmlnrpsdnghtpfg
    diflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwlliyhgvtltcngy
    vysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaalcdadtgrvaiyy
    gaadthvalafgyideivdfvkrns
    

  • Chain 'F':
    Sequence, based on SEQRES records: (download)
    >1vkdF (F:)
    mgsdkihhhhhhmkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsa
    vvpyngefvgvfridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydpr
    vvkiedtyyitfctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvml
    nrpsdnghtpfgdiflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwll
    iyhgvtltcngyvysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaal
    cdadtgrvaiyygaadthvalafgyideivdfvkrnsm
    

    Sequence, based on observed residues (ATOM records): (download)
    >1vkdF (F:)
    mkvftekipnipweerpegytgpvwrysknpiigrnpvpkgarvfnsavvpyngefvgvf
    ridhkntrpflhfgrskdginweiepeeiqwvdvngepfqpsyaydprvvkiedtyyitf
    ctddhgptigvgmtkdfktfvrlpnayvpfnrngvlfprkingkyvmlnrpsdnghtpfg
    diflsespdmihwgnhrfvlgrssynwwenlkigagpypietsegwlliyhgvtltcngy
    vysfgaalldlddpskvlyrsryylltpeeeyetvgfvpnvvfpcaalcdadtgrvaiyy
    gaadthvalafgyideivdfvkrnsm