Structure of PDB 5xd2 Chain A Binding Site BS03

Receptor Information

>5xd2 Chain A (length=292) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

KHTVRAAGAVLWRDPATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAR
EIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDK
LVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYK
GDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQEL
DQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIE
WWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 5xd2 Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xd2 Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): K65 E85
• Binding residue (residue number reindexed from 1): K35 E55
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T23 A29
• Catalytic site (residue number reindexed from 1): T3 A9
• Enzyme Commision number: 3.6.1.58: 8-oxo-dGDP phosphatase.
  3.6.1.61: diadenosine hexaphosphate hydrolase (ATP-forming).
  3.6.1.69: 8-oxo-(d)GTP phosphatase.

Gene Ontology

Molecular Function

• GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
• GO:0016787 hydrolase activity
• GO:0044715 8-oxo-dGDP phosphatase activity
• GO:0044716 8-oxo-GDP phosphatase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006260 DNA replication
• GO:0006281 DNA repair

External links

• PDB: RCSB:5xd2, PDBe:5xd2, PDBj:5xd2
• PDBsum: 5xd2
• PubMed: 28705712
• UniProt: A0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)