Structure of PDB 5xd5 Chain A Binding Site BS03

Receptor Information

>5xd5 Chain A (length=289) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

TVRAAGAVLWRDATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREIH
EETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLVW
LPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGDD
RKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQL
IHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWWC
ERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5xd5 Chain A Residue 406

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5xd5 Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1
• Resolution: 1.75 Å
• Binding residue (original residue number in PDB): E81 E85 E127
• Binding residue (residue number reindexed from 1): E48 E52 E94
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): T23 A29
• Catalytic site (residue number reindexed from 1): T1 A7
• 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:5xd5, PDBe:5xd5, PDBj:5xd5
• PDBsum: 5xd5
• PubMed: 28705712
• UniProt: A0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)