Structure of PDB 3ef5 Chain A Binding Site BS01

Receptor Information
>3ef5 Chain A (length=132) Species: 959 (Bdellovibrio bacteriovorus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALAR
ELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMML
EWIHPEELKHRNIPEANRKILHKIYKALGLEW
Ligand information
Ligand IDDGT
InChIInChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyHAAZLUGHYHWQIW-KVQBGUIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H16 N5 O13 P3
Name2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL477486
DrugBankDB02181
ZINCZINC000008215755
PDB chain3ef5 Chain A Residue 3800 [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]
PDB3ef5 Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		V24 R40 F52 G54 G55 K56 I99 P133 N136
Binding residue
(residue number reindexed from 1)		V5 R21 F33 G35 G36 K37 I80 P114 N117
Annotation score2
Enzymatic activity
Enzyme Commision number 3.6.1.55: 8-oxo-dGTP diphosphatase.
Gene Ontology
Molecular Function
GO:0005525 GTP binding
GO:0008413 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0035539 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity
GO:0042802 identical protein binding
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:3ef5, PDBe:3ef5, PDBj:3ef5
PDBsum3ef5
PubMed19278661
UniProtQ6MPX4

[Back to BioLiP]