Structure of PDB 6iod Chain A Binding Site BS02

Receptor Information
>6iod Chain A (length=212) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMAGAQDFVPHTADLAELAAAAGECRGCGLYRDATQAVFGAGGRSARI
MMIGEQPGDKEDLAGLPFVGPAGRLLDRALEAADIDRDALYVTNAVKHFK
FTRAAGGKRRIHKTPSRTEVVACRPWLIAEMTSVEPDVVVLLGATAAKAL
LGNDFRVTQHRGEVLHVDDVPGDPALVATVHPSSLLRGPKEERESAFAGL
VDDLRVAADVRP
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 chain6iod Chain A Residue 301 [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]
PDB6iod Suicide inactivation of the uracil DNA glycosylase UdgX by covalent complex formation.
Resolution1.66 Å
Binding residue
(original residue number in PDB)		C24 G26 C27 K94 H95 C120 W123
Binding residue
(residue number reindexed from 1)		C27 G29 C30 K97 H98 C123 W126
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0004844 uracil DNA N-glycosylase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
GO:0097506 deaminated base DNA N-glycosylase activity
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6iod, PDBe:6iod, PDBj:6iod
PDBsum6iod
PubMed31101915
UniProtI7F541

[Back to BioLiP]