Structure of PDB 7vf6 Chain B Binding Site BS03

Receptor Information
>7vf6 Chain B (length=366) Species: 2759389 (Gordonia phage Archimedes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSAIDVIVGGQFGSEAKGRVTLERVQHWADNGHAVASMRVAGPNAGHVVW
DQGHRFAMRSLPVGFVDPGTDLYIAAGSEVDIEVLQQEVDLVESYGYEVR
DRLYIHPQATWLEPVHRDREASSTLTAKVGSTSKGIGAARSDRIWRVANL
VGDNPAFQELGRVSDFTEDLRSELVDGSLALVIEGTQGYGLGLHAGHYPQ
CTSSDARAIDFLAMAGINPWDLSREDLAAHGFRIHVVIRPFPIRVAGNSG
ELSGETSWDELGLEAERTTVTNKIRRVGQFDPELVRRAVLANGVNNVKIH
LSMADQLIPQLAGLEDLPEGWRESEYAGRLREFIDQIPFNERLVSLGTGP
HTRIELFKENLYFQLE
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain7vf6 Chain B Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7vf6 Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage.
Resolution1.703 Å
Binding residue
(original residue number in PDB)		S15 A17 K18 G19 R20 G47 H48 V49 M304 D306 G348 G350 P351
Binding residue
(residue number reindexed from 1)		S14 A16 K17 G18 R19 G46 H47 V48 M303 D305 G347 G349 P350
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.4.25: 2-amino-2'-deoxyadenylo-succinate synthase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004019 adenylosuccinate synthase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0006164 purine nucleotide biosynthetic process
GO:0044208 'de novo' AMP biosynthetic process
GO:0046040 IMP metabolic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7vf6, PDBe:7vf6, PDBj:7vf6
PDBsum7vf6
PubMed37308591
UniProtA0A7L7SI10

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