Structure of PDB 3ffu Chain A Binding Site BS01

Receptor Information
>3ffu Chain A (length=133) Species: 959 (Bdellovibrio bacteriovorus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GHWIPVVAGFLRKDGKILVGQRPENNSLAGQWEFPGGKIENGETPEEALA
RELNEELGIEAEVGELKLACTHSYGDVGILILFYEILYWKGEPRAKHHMM
LEWIHPEELKHRNIPEANRKILHKIYKALGLEW
Ligand information
Ligand IDGTP
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H,24,25)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyXKMLYUALXHKNFT-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1[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=C(NC2=O)N
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL1233147
DrugBankDB04137
ZINCZINC000060094177
PDB chain3ffu Chain A Residue 4033 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ffu Structure and Biological Function of the RNA Pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		V24 R40 E51 F52 G54 G55 K56 E70 I97 P133 N136
Binding residue
(residue number reindexed from 1)		V6 R22 E33 F34 G36 G37 K38 E52 I79 P115 N118
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=6.44,Kd=0.36uM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:3ffu, PDBe:3ffu, PDBj:3ffu
PDBsum3ffu
PubMed19278661
UniProtQ6MPX4

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