Structure of PDB 6fm0 Chain B Binding Site BS01

Receptor Information
>6fm0 Chain B (length=290) Species: 1076759 (Vibrio phage phiVC8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENVDLVIDLQFGSTGKGLIAGYLAEKNGYDTVINANMPNAGHTYINAEGR
KWMHKVLPNGIVSPNLKRVMLGAGSVFSINRLMEEIEMSKDLLHDKVAIL
IHPMATVLDGSMAAMVEKLQRDPTNNTIVARDVAQYDGRIAQYVCTVEEW
DMALMASERILAEGAQGFSLSLNQEFYPYCTSRDCTPARFLADMGIPLPM
LNKVIGTARCHPIRVGHYPDQEERRVFSFSFIQMQKAMWTCQPDEVFLNF
CNYLSPQDIVHQIEVAAQSRYCDAEVKYLGFGPTFNDVEL
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 chain6fm0 Chain B Residue 401 [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]
PDB6fm0 A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S14 G16 K17 H43 T44 F295 G330 P331
Binding residue
(residue number reindexed from 1)		S13 G15 K16 H42 T43 F250 G282 P283
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) S14 K17 G42 H43 Q187
Catalytic site (residue number reindexed from 1) S13 K16 G41 H42 Q166
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6fm0, PDBe:6fm0, PDBj:6fm0
PDBsum6fm0
PubMed33926955
UniProtG3FFN6|PURZ_BPVC8 N6-succino-2-amino-2'-deoxyadenylate synthase (Gene Name=purZ)

[Back to BioLiP]