Structure of PDB 1tdz Chain A Binding Site BS03

Receptor Information
>1tdz Chain A (length=265) Species: 1358 (Lactococcus lactis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQG
ISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFADG
QLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRK
STKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLH
DSIIEILQKAIKLGGSSILGSTGKMQNELQVYGKTGEKCSRCGAEIQKIK
VAGRGTHFCPVCQQK
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain1tdz Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1tdz Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase
Resolution1.8 Å
Binding residue
(original residue number in PDB)		C245 C248 C265 C268
Binding residue
(residue number reindexed from 1)		C239 C242 C259 C262
Annotation score1
Enzymatic activity
Enzyme Commision number 3.2.2.23: DNA-formamidopyrimidine glycosylase.
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
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:1tdz, PDBe:1tdz, PDBj:1tdz
PDBsum1tdz
PubMed15249553
UniProtP42371|FPG_LACLC Formamidopyrimidine-DNA glycosylase (Gene Name=mutM)

[Back to BioLiP]