PDB entry 2vkd

View 2vkd on RCSB PDB site
Description: crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp-glc and manganese ion
Class: toxin
Keywords: toxin, glycosyltransferase
Deposited on 2007-12-18, released 2008-03-18
The last revision prior to the SCOPe 2.02 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-31.
Experiment type: XRAY
Resolution: 2.53 Å
R-factor: 0.247
AEROSPACI score: 0.27 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: cytotoxin l
    Species: CLOSTRIDIUM SORDELLII [TaxId:1505]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q46342 (0-End)
      • engineered mutation (12)
      • engineered mutation (288)
    Domains in SCOPe 2.02: d2vkda1
  • Chain 'B':
    Compound: cytotoxin l
    Species: CLOSTRIDIUM SORDELLII [TaxId:1505]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q46342
      • engineered mutation (12)
      • engineered mutation (288)
    Domains in SCOPe 2.02: d2vkdb_
  • Chain 'C':
    Compound: cytotoxin l
    Species: CLOSTRIDIUM SORDELLII [TaxId:1505]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q46342 (0-End)
      • engineered mutation (12)
      • engineered mutation (288)
    Domains in SCOPe 2.02: d2vkdc_
  • Heterogens: MN, UPG, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2vkdA (A:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
galged

    Sequence, based on observed residues (ATOM records): (download) 
    >2vkdA (A:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
ga

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2vkdB (B:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
galged

    Sequence, based on observed residues (ATOM records): (download) 
    >2vkdB (B:)
lvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnylnt
ykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkdvn
sdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiydk
qkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndirn
lekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfksin
kpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseiflp
lddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsinegt
dfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqdll
mfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2vkdC (C:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
galged

    Sequence, based on observed residues (ATOM records): (download) 
    >2vkdC (C:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
g