Structure of PDB 1del Chain B Binding Site BS03

Receptor Information
>1del Chain B (length=231) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKLIFLSGVKRSGKDTTADFIMSNYSAVKYQLAGPIKDALAYAWGVFAAN
TDYPCLTRKEFEGIDYDRETNLNLTKLEVITIMEQAFCYLNGKSPIKGVF
VFDDEGKESVNFVAFNKITDVINNIEDQWSVRRLMQALGTDLIVNNFDRM
YWVKLFALDYLDKFNSGYDYYIVPDTRQDHEMDAARAMGATVIHVVRPGA
GLPIRDGDLVITNDGSLEELFSKIKNTLKVL
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain1del Chain B Residue 302 [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]
PDB1del Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R11 G13 D15 T16 N223 G225 S226 L227
Binding residue
(residue number reindexed from 1)		R11 G13 D15 T16 N213 G215 S216 L217
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D15 R68
Catalytic site (residue number reindexed from 1) D15 R68
Enzyme Commision number 2.7.4.13: (deoxy)nucleoside-phosphate kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0047507 (deoxy)nucleoside-phosphate kinase activity
Biological Process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1del, PDBe:1del, PDBj:1del
PDBsum1del
PubMed8670851
UniProtP04531|DNMK_BPT4 Deoxynucleotide monophosphate kinase (Gene Name=1)

[Back to BioLiP]