Structure of PDB 8iip Chain A Binding Site BS02

Receptor Information

>8iip Chain A (length=206) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

AGAQDFVPHTADLAELAAAAGECRGCGLYRDATQAVFGAGGRSARIMMIG
EQPGDKEDLAGLPFVGPAGRLLDRALEAADIDRDALYVTNAVKHFKFTRA
AGGKRRIQKTPSRTEVVACRPWLIAEMTSVEPDVVVLLGATAAKALLGND
FRVTQHRGEVLHVDDVPGDPALVATVHPSSLLRGPKEERESAFAGLVDDL
RVAADV

Ligand information

• Ligand ID: URA
• InChI: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)
• InChIKey: ISAKRJDGNUQOIC-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: O=C1NC=CC(=O)N1
  ACDLabs 10.04: O=C1C=CNC(=O)N1
  OpenEye OEToolkits 1.5.0: C1=CNC(=O)NC1=O
• Formula: C4 H4 N2 O2
• Name: URACIL
• ChEMBL: CHEMBL566
• DrugBank: DB03419
• ZINC: ZINC000000895045
• PDB chain: 8iip Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8iip Mutational and structural analyses of UdgX: insights into the active site pocket architecture and its evolution.
• Resolution: 1.63 Å
• Binding residue (original residue number in PDB): E52 Q53 E58 P64 F65 N91 H178
• Binding residue (residue number reindexed from 1): E51 Q52 E57 P63 F64 N90 H177
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.2.27: uracil-DNA glycosylase.

Gene Ontology

Molecular Function

• GO:0004844 uracil DNA N-glycosylase 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

External links

• PDB: RCSB:8iip, PDBe:8iip, PDBj:8iip
• PDBsum: 8iip
• PubMed: 37283083
• UniProt: A0QP43