Structure of PDB 7ody Chain A Binding Site BS01

Receptor Information
>7ody Chain A (length=99) Species: 260586 (Cyanophage S-2L) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PATVAELQAEIAAWIHPLNPDRRPGGTIAKLLEEIGELIASDRDPLEVAD
VLILALDLATLLGVDVTEAIRAKLAINRARSWARADNGAMRHIPGSDTP
Ligand information
Ligand IDDGI
InChIInChI=1S/C10H15N5O10P2/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(24-6)2-23-27(21,22)25-26(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyCIKGWCTVFSRMJU-KVQBGUIXSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O3
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O10 P2
Name2'-DEOXYGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL1232205
DrugBankDB03491
ZINCZINC000008215878
PDB chain7ody Chain A Residue 201 [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]
PDB7ody Characterization of a triad of genes in cyanophage S-2L sufficient to replace adenine by 2-aminoadenine in bacterial DNA.
Resolution1.43 Å
Binding residue
(original residue number in PDB)		I16 K31 E35 E38 D53 L57 D60
Binding residue
(residue number reindexed from 1)		I15 K30 E34 E37 D50 L54 D57
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.1.9: nucleotide diphosphatase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0016787 hydrolase activity
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:7ody, PDBe:7ody, PDBj:7ody
PDBsum7ody
PubMed34354070
UniProtA0A7U3TBV3|DGTPH_BPS2L dATP/dGTP diphosphohydrolase (Gene Name=S2L_23)

[Back to BioLiP]