PDB entry 6gdr

View 6gdr on RCSB PDB site
Description: dna binding with a minimal scaffold: structure-function analysis of lig e dna ligases
Deposited on 2018-04-24, released 2018-07-25
The last revision was dated 2018-10-03, with a file datestamp of 2018-09-28.
Experiment type: XRAY
Resolution: 2.33 Å
R-factor: N/A
AEROSPACI score: 0.24 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: DNA ligase
    Species: Alteromonas mediterranea [TaxId:314275]
    Gene: BM525_03130
    Database cross-references and differences (RAF-indexed):
    • Uniprot A0A1J0SCU0
      • conflict (17)
      • conflict (55)
      • conflict (127)
      • conflict (207)
      • conflict (223-224)
      • conflict (258)
      • conflict (263)
  • Chain 'B':
    Compound: DNA (5'-d(*tp*tp*cp*cp*gp*ap*tp*ap*gp*tp*gp*gp*gp*gp*tp*cp*gp*cp*ap*ap*t)-3')
    Species: Alteromonas mediterranea [TaxId:314275]
  • Chain 'C':
    Compound: DNA
    Species: Alteromonas mediterranea [TaxId:314275]
  • Chain 'D':
    Compound: DNA (5'-d(p*cp*ap*cp*tp*ap*tp*cp*gp*gp*ap*a)-3')
    Species: Alteromonas mediterranea [TaxId:314275]
  • Heterogens: PO4, AMP, HOH

PDB Chain Sequences:
This PDB entry is not classified in SCOPe 2.08, so the chain sequences below are not included in the ASTRAL sequence sets.

  • Chain 'A':
    Sequence, based on SEQRES records:
    >6gdrA (A:)
gedkhdivdglqlakqyghsrqdiniaeywvsekldgirarwdgtelrtrnnnkidapaw
ftanwpkatidgelwiargqfertasivlskltsvapqsvagslprtestvdamtathsl
pskrwakvrfmafdmpvagqsfdsrlnmlnnlkeatpnptfavvsqftlssvnaleekle
qvtlsggeglmlhhkkafyhsgrsdklikvkqfedaeakvlahfagkgkfkgmmgsllve
tpagvqfklgtgfsekerrappavgswvtfkfygvtkngkprfasflrvrppsdlpk

    Sequence, based on observed residues (ATOM records):
    >6gdrA (A:)
ivdglqlakqyghqdiniaeywvsekldgirarwdgtelrtrnnnkidapawftanwpka
tidgelwiargqfertasivlskltlpskrwakvrfmafdmpvagqsfdsrlnmlnnlke
atpnptfavvsqftlssvnaleekleqvtlsggeglmlhhkkafyhsgrsdklikvkqfe
daeakvlahfagkgkfkgmmgsllvetpagvqfklgtgfsekerrappavgswvtfkfyg
vtkngkprfasflrvr

  • Chain 'B':
    No sequence available.

  • Chain 'C':
    No sequence available.

  • Chain 'D':
    No sequence available.