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 2.06 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: 0.164
AEROSPACI score: 0.45 (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 2.06: 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 2.06: 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 2.06: 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 2.06: 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 2.06: 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 2.06: 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