Structure of PDB 5ggb Chain A Binding Site BS01

Receptor Information
>5ggb Chain A (length=290) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HTVRAAGAVLWRDATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAAREI
HEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVDKLV
WLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRYKGD
DRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQELDQ
LIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLIEWW
CERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK
Ligand information
Ligand ID8GD
InChIInChI=1S/C10H15N5O11P2/c11-9-13-7-6(8(17)14-9)12-10(18)15(7)5-1-3(16)4(25-5)2-24-28(22,23)26-27(19,20)21/h3-5,16H,1-2H2,(H,12,18)(H,22,23)(H2,19,20,21)(H3,11,13,14,17)/t3-,4+,5+/m0/s1
InChIKeyLJMLTZSNWOCYNQ-VPENINKCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=O)CO[P@](=O)(O)OP(=O)(O)O)O
CACTVS 3.352NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)N1
CACTVS 3.352NC1=NC2=C(NC(=O)N2[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3)C(=O)N1
OpenEye OEToolkits 1.7.0C1C(C(OC1N2C3=C(C(=O)NC(=N3)N)NC2=O)COP(=O)(O)OP(=O)(O)O)O
FormulaC10 H15 N5 O11 P2
Name2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate);
8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-diphosphate
ChEMBL
DrugBank
ZINCZINC000058638349
PDB chain5ggb Chain A Residue 401 [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]
PDB5ggb Biochemical and structural studies of Mycobacterium smegmatis MutT1, a sanitization enzyme with unusual modes of association
Resolution1.1 Å
Binding residue
(original residue number in PDB)		R169 H170 R176 R186 R218 E242 Q271 G272 K273 K297
Binding residue
(residue number reindexed from 1)		R137 H138 R144 R154 R186 E210 Q239 G240 K241 K265
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T23 A29
Catalytic site (residue number reindexed from 1) T2 A8
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ggb, PDBe:5ggb, PDBj:5ggb
PDBsum5ggb
PubMed28375146
UniProtA0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)

[Back to BioLiP]