Structure of PDB 6rok Chain A

Receptor sequence
>6rokA (length=271) Species: 1359 (Lactococcus cremoris) [Search protein sequence]
PELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQ
GISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFAD
GQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLR
KSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLL
HDSIIEILQKAIKLGGSSIRTYSALGSTGKMQNELQVYGKTGEKCSRCGA
EIQKIKVAGRGTHFCPVCQQK
3D structure
PDB6rok Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights.
ChainA
Resolution1.95 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) P1 E2
Catalytic site (residue number reindexed from 1) P1 E2
Enzyme Commision number 3.2.2.23: DNA-formamidopyrimidine glycosylase.
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
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 A P1 E2 K57 H72 R74 M75 K129 G170 N171 Y238 K254 K256 R260 P1 E2 K57 H72 R74 M75 K129 G170 N171 Y238 K254 K256 R260
BS02 dna A K90 H91 V108 R109 K110 F111 K90 H91 V108 R109 K110 F111
BS03 ZN A C245 C248 C265 C268 C245 C248 C265 C268
BS04 5JL A L161 E162 L161 E162
Gene Ontology
Molecular Function
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:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity
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:0034039 8-oxo-7,8-dihydroguanine 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

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:6rok, PDBe:6rok, PDBj:6rok
PDBsum6rok
PubMed32192183
UniProtP42371|FPG_LACLC Formamidopyrimidine-DNA glycosylase (Gene Name=mutM)

[Back to BioLiP]