PDB entry 2vkh

View 2vkh on RCSB PDB site
Description: crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp-glc and calcium ion
Class: toxin
Keywords: toxin, glycosyltransferase
Deposited on 2007-12-19, released 2008-03-18
The last revision prior to the SCOP 1.75 freeze date was dated 2008-04-08, with a file datestamp of 2008-04-04.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.23586
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: cytotoxin l
    Species: CLOSTRIDIUM SORDELLII
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q46342 (0-End)
      • engineered mutation (12)
      • engineered mutation (288)
    Domains in SCOP 1.75: d2vkha1
  • Chain 'B':
    Compound: cytotoxin l
    Species: CLOSTRIDIUM SORDELLII
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q46342
      • engineered mutation (12)
      • engineered mutation (288)
    Domains in SCOP 1.75: d2vkhb1
  • Chain 'C':
    Compound: cytotoxin l
    Species: CLOSTRIDIUM SORDELLII
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q46342 (0-End)
      • engineered mutation (12)
      • engineered mutation (288)
    Domains in SCOP 1.75: d2vkhc1
  • Heterogens: CA, UPG, HOH

PDB Chain Sequences:

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

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

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

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

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

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