Structure of PDB 8d2m Chain A Binding Site BS01

Receptor Information
>8d2m Chain A (length=224) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AGRFAQSQTREDYLALLAEDIERDIPYDPEPIGRYNVAPGTKVLLLSERD
EHLHLDPVFWGYAPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFAD
GWFEWKKEGDKKQPFFIYRADGQPIFMAAIGSTPFERGDEAEGFLIVTAA
ADQGLVDIHDRRPLVLSPEAAREWMRQEISGKEASEIAASGCVPANQFSW
HPVSRAVGNVKNQGAELIQPVLEV
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8d2m The SOS response-associated peptidase (SRAP) domain of YedK catalyzes ring opening of abasic sites and reversal of its DNA-protein cross-link.
Resolution1.821 Å
Binding residue
(original residue number in PDB)		A2 G3 R4 P40 W67 I74 N75 R77 S84 R85 M86 F87 W106 K113 T149 H160 R162 G209
Binding residue
(residue number reindexed from 1)		A1 G2 R3 P39 W66 I73 N74 R76 S83 R84 M85 F86 W105 K112 T148 H159 R161 G208
Enzymatic activity
Enzyme Commision number 3.4.-.-
4.-.-.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003697 single-stranded DNA binding
GO:0008233 peptidase activity
GO:0016829 lyase activity
GO:0160129 protein-DNA covalent cross-linking activity
Biological Process
GO:0006508 proteolysis
GO:0006974 DNA damage response
GO:0009432 SOS response
GO:0106300 protein-DNA covalent cross-linking repair

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Molecular Function
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Biological Process
External links
PDB RCSB:8d2m, PDBe:8d2m, PDBj:8d2m
PDBsum8d2m
PubMed35934051
UniProtP76318|YEDK_ECOLI Abasic site processing protein YedK (Gene Name=yedK)

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