PDB entry 2ivk

View 2ivk on RCSB PDB site
Description: Crystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA
Class: hydrolase
Keywords: DNAse, endonuclease, DNA hydrolysis, protein nucleic acid interactions, DNA cleavage preference, hydrolase
Deposited on 2006-06-14, released 2007-01-02
The last revision prior to the SCOPe 2.07 freeze date was dated 2017-03-29, with a file datestamp of 2017-03-24.
Experiment type: XRAY
Resolution: 2.9 Å
R-factor: N/A
AEROSPACI score: 0.13 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: endonuclease I
    Species: Vibrio vulnificus [TaxId:672]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7MHK3 (0-End)
      • engineered mutation (61)
    Domains in SCOPe 2.07: d2ivka_
  • Chain 'B':
    Compound: endonuclease I
    Species: Vibrio vulnificus [TaxId:672]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7MHK3 (0-212)
      • engineered mutation (61)
    Domains in SCOPe 2.07: d2ivkb_
  • Chain 'C':
    Compound: endonuclease I
    Species: Vibrio vulnificus [TaxId:672]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7MHK3 (0-212)
      • engineered mutation (61)
    Domains in SCOPe 2.07: d2ivkc_
  • Chain 'D':
    Compound: endonuclease I
    Species: Vibrio vulnificus [TaxId:672]
    Database cross-references and differences (RAF-indexed):
    • Uniprot Q7MHK3 (0-End)
      • engineered mutation (61)
    Domains in SCOPe 2.07: d2ivkd_
  • Chain 'E':
    Compound: 5'-d(*gp*ap*ap*tp*tp*cp*gp*ap*tp*cp *gp*ap*ap*tp*t)-3'
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'F':
    Compound: 5'-d(*ap*ap*tp*tp*cp*gp*ap*tp*cp*gp *ap*ap*tp*tp*c)-3'
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'G':
    Compound: 5'-d(*gp*ap*ap*tp*tp*cp*gp*ap*tp*cp *gp*ap*ap*tp*t)-3'
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'H':
    Compound: 5'-d(*ap*ap*tp*tp*cp*gp*ap*tp*cp*gp *ap*ap*tp*tp*c)-3'
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'I':
    Compound: 5'-d(*gp*ap*ap*tp*tp*cp*gp*ap*tp*cp *gp*ap*ap*tp*tp*c)-3'
    Species: synthetic construct, synthetic [TaxId:32630]
  • Chain 'J':
    Compound: 5'-d(*gp*ap*ap*tp*tp*cp*gp*ap*tp*cp *gp*ap*ap*tp*tp*c)-3'
    Species: synthetic construct, synthetic [TaxId:32630]
  • Heterogens: HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >2ivkA (A:)
appssfsaakqqavkiyqdhpisfycgcdiewqgkkgipnletcgyqvrkqqtrasriew
eavvpawqfghhrqcwqkggrkncskndqqfrlmeadlhnltpaigevngdrsnfnfsqw
ngvdgvsygrcemqvnfkqrkvmppdrargsiartylymsqeygfqlskqqqqlmqawnk
sypvdewectrddriakiqgnhnpfvqqscqtq

    Sequence, based on observed residues (ATOM records): (download) 
    >2ivkA (A:)
appssfsaakqqavkiyqdhpisfycgcdiewqgkkgipnletcgyqvrkqqtrasriew
eavvpawqfghhrqcwqkggrkncskndqqfrlmeadlhnltpaigevngdrsnfnfsqw
ngvdgvsygrcemqvnfkqrkvmppdrargsiartylymsqeygfqlskqqqqlmqawnk
sypvdewectrddriakiqgnhnpfvqqscq

  • Chain 'B':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ivkB (B:)
appssfsaakqqavkiyqdhpisfycgcdiewqgkkgipnletcgyqvrkqqtrasriew
eavvpawqfghhrqcwqkggrkncskndqqfrlmeadlhnltpaigevngdrsnfnfsqw
ngvdgvsygrcemqvnfkqrkvmppdrargsiartylymsqeygfqlskqqqqlmqawnk
sypvdewectrddriakiqgnhnpfvqqscqtq

  • Chain 'C':
    Sequence; same for both SEQRES and ATOM records: (download) 
    >2ivkC (C:)
appssfsaakqqavkiyqdhpisfycgcdiewqgkkgipnletcgyqvrkqqtrasriew
eavvpawqfghhrqcwqkggrkncskndqqfrlmeadlhnltpaigevngdrsnfnfsqw
ngvdgvsygrcemqvnfkqrkvmppdrargsiartylymsqeygfqlskqqqqlmqawnk
sypvdewectrddriakiqgnhnpfvqqscqtq

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >2ivkD (D:)
appssfsaakqqavkiyqdhpisfycgcdiewqgkkgipnletcgyqvrkqqtrasriew
eavvpawqfghhrqcwqkggrkncskndqqfrlmeadlhnltpaigevngdrsnfnfsqw
ngvdgvsygrcemqvnfkqrkvmppdrargsiartylymsqeygfqlskqqqqlmqawnk
sypvdewectrddriakiqgnhnpfvqqscqtq

    Sequence, based on observed residues (ATOM records): (download) 
    >2ivkD (D:)
appssfsaakqqavkiyqdhpisfycgcdiewqgkkgipnletcgyqvrkqqtrasriew
eavvpawqfghhrqcwqkggrkncskndqqfrlmeadlhnltpaigevngdrsnfnfsqw
ngvdgvsygrcemqvnfkqrkvmppdrargsiartylymsqeygfqlskqqqqlmqawnk
sypvdewectrddriakiqgnhnpfvqqscq

  • Chain 'E':
    No sequence available.

  • Chain 'F':
    No sequence available.

  • Chain 'G':
    No sequence available.

  • Chain 'H':
    No sequence available.

  • Chain 'I':
    No sequence available.

  • Chain 'J':
    No sequence available.