Structure of PDB 1k3w Chain A Binding Site BS01

Receptor Information

>1k3w Chain A (length=254) Species: 562 (Escherichia coli)

PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETR
GKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTI
LLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRN
RQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHA
LLEIPRFSYATRGQALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCP
GCQH

Ligand information

>1k3w Chain B (length=8)

tcatcctg

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1k3w Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate.
• Resolution: 1.42 Å
• Binding residue (original residue number in PDB): Q69 Y71 R87 V88 R90 S104 S106
• Binding residue (residue number reindexed from 1): Q69 Y71 R87 V88 R90 S104 S106

Enzymatic activity

• Enzyme Commision number: 3.2.2.-
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
• GO:0016829 lyase activity
• GO:0019104 DNA N-glycosylase activity
• GO:0046872 metal ion binding
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:1k3w, PDBe:1k3w, PDBj:1k3w
• PDBsum: 1k3w
• PubMed: 11847126
• UniProt: P50465|END8_ECOLI Endonuclease 8 (Gene Name=nei)