Structure of PDB 8d2m Chain B

Receptor sequence
>8d2mB (length=222) Species: 562 (Escherichia coli) [Search protein sequence]
AGRFAQSQTREDYLALLAERDIPYDPEPIGRYNVAPGTKVLLLSERDEHL
HLDPVFWGYAPGWWDKPPLINARVETAATSRMFKPLWQHGRAICFADGWF
EWKKEGDKKQPFFIYRADGQPIFMAAIGSTPFERGDEAEGFLIVTAAADQ
GLVDIHDRRPLVLSPEAAREWMRQEISGKEASEIAASGCVPANQFSWHPV
SRAVGNVKNQGAELIQPVLEVL
3D structure
PDB8d2m The SOS response-associated peptidase (SRAP) domain of YedK catalyzes ring opening of abasic sites and reversal of its DNA-protein cross-link.
ChainB
Resolution1.821 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 3.4.-.-
4.-.-.-
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna B A2 G3 R4 P40 W67 K70 I74 N75 R77 S84 R85 M86 F87 W106 K113 T149 H160 R162 G209 A1 G2 R3 P36 W63 K66 I70 N71 R73 S80 R81 M82 F83 W102 K109 T145 H156 R158 G205
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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