PDB entry 2vl8

View 2vl8 on RCSB PDB site
Description: crystal structure of the catalytic domain of lethal toxin from clostridium sordellii in complex with udp, castanospermine and calcium ion
Class: toxin
Keywords: toxin, glycosyltransferase
Deposited on 2008-01-09, released 2008-06-17
The last revision prior to the SCOPe 2.08 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-31.
Experiment type: XRAY
Resolution: 2.31 Å
R-factor: 0.218
AEROSPACI score: 0.34 (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 2.08: d2vl8a_
  • 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 2.08: d2vl8b_
  • 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 2.08: d2vl8c_
  • Heterogens: UDP, CTS, CA, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2vl8A (A:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
galged

    Sequence, based on observed residues (ATOM records): (download) 
    >2vl8A (A:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsaraksqfeeykkgyfega

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >2vl8B (B:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
galged

    Sequence, based on observed residues (ATOM records): (download) 
    >2vl8B (B:)
lvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnylnt
ykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkdvn
sdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiydk
qkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndirn
lekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfksin
kpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseiflp
lddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsinegt
dfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqdll
mfkdnstnihllepelrnfefpktkisqlteqeitslaraksqfeeykkgyfe

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >2vl8C (C:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwsfnqaraksqfeeykkgyfe
galged

    Sequence, based on observed residues (ATOM records): (download) 
    >2vl8C (C:)
mnlvnkaqlqkmayvkfriqedeyvailnaleeyhnmsessvvekylklkdinnltdnyl
ntykksgrnkalkkfkeyltmevlelknnsltpveknlhfiwiggqindtainyinqwkd
vnsdytvkvfydsnaflintlkktivesatnntlesfrenlndpefdynkfyrkrmeiiy
dkqkhfidyyksqieenpefiidniiktylsneyskdlealnkyieeslnkitanngndi
rnlekfadedlvrlynqelverwnlaaasdilrismlkedggvyldvdmlpgiqpdlfks
inkpdsitntswemikleaimkykeyipgytsknfdmldeevqrsfesalssksdkseif
lplddikvsplevkiafannsvinqalislkdsycsdlvinqiknrykilndnlnpsine
gtdfnttmkifsdklasisnednmmfmikitnylkvgfapdvrstinlsgpgvytgayqd
llmfkdnstnihllepelrnfefpktkisqlteqeitslwaraksqfeeykkgyfeg