Structure of PDB 5xd4 Chain A Binding Site BS01

Receptor Information
>5xd4 Chain A (length=293) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KHTVRAAGAVLWRDAPATVEVAVIHRPRYDDWSLPKGKLDQGETEPVAAA
REIHEETGHTAVLGRRLGRVTYPIPQGTKRVWYWAAKSTGGDFSPNDEVD
KLVWLPVDAAMDQLQYPDDRKVLRRFVKRPVDTKTVLVVRHGTAGRRSRY
KGDDRKRPLDKRGRAQAEALVAQLMAFGATTLYAADRVRCHQTIEPLAQE
LDQLIHNEPLLTEEAYAADHKAARKRLLEIAGRPGNPVICTQGKVIPGLI
EWWCERAKVRPETTGNRKGSTWVLSLSDGELVGADYLSPPDEK
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5xd4 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5xd4 Hydrolysis of diadenosine polyphosphates. Exploration of an additional role of Mycobacterium smegmatis MutT1
Resolution1.47 Å
Binding residue
(original residue number in PDB)		R55 Y58 K65 K67 Y101 K108 Y145
Binding residue
(residue number reindexed from 1)		R26 Y29 K36 K38 Y72 K79 Y116
Annotation score5
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5xd4, PDBe:5xd4, PDBj:5xd4
PDBsum5xd4
PubMed28705712
UniProtA0QUZ2|MUTT1_MYCS2 8-oxo-(d)GTP phosphatase (Gene Name=mutT1)

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