Structure of PDB 4ypr Chain A Binding Site BS04

Receptor Information
>4ypr Chain A (length=355) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVI
PYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTR
YGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMRVLSRLF
LVTDDIAKCSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSC
LLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRK
RDSTGLLANLWEFPSCETDGADGKEKLEQMVGEQYGLQVELTEPIVSFEH
AFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREY
KEWAS
Ligand information
Ligand IDSF4
InChIInChI=1S/4Fe.4S
InChIKeyLJBDFODJNLIPKO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7[S]12[Fe]3[S]4[Fe]1[S]5[Fe]2[S]3[Fe]45
CACTVS 3.385S1[Fe]S[Fe]1.S2[Fe]S[Fe]2
FormulaFe4 S4
NameIRON/SULFUR CLUSTER
ChEMBL
DrugBank
ZINC
PDB chain4ypr Chain A Residue 400 [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]
PDB4ypr Structural Basis for Avoidance of Promutagenic DNA Repair by MutY Adenine DNA Glycosylase.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		R153 C198 P203 C205 C208 C214
Binding residue
(residue number reindexed from 1)		R148 C193 P198 C200 C203 C209
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E43 Y126 N144
Catalytic site (residue number reindexed from 1) E38 Y121 N139
Enzyme Commision number 3.2.2.31: adenine glycosylase.
Gene Ontology
Molecular Function
GO:0000701 purine-specific mismatch base pair DNA N-glycosylase activity
GO:0003677 DNA binding
GO:0003824 catalytic activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0019104 DNA N-glycosylase activity
GO:0032357 oxidized purine DNA binding
GO:0034039 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
GO:0035485 adenine/guanine mispair binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006298 mismatch repair
GO:0006950 response to stress

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4ypr, PDBe:4ypr, PDBj:4ypr
PDBsum4ypr
PubMed25995449
UniProtP83847|MUTY_GEOSE Adenine DNA glycosylase (Gene Name=mutY)

[Back to BioLiP]