Structure of PDB 5zwa Chain A Binding Site BS01

Receptor Information
>5zwa Chain A (length=264) Species: 28901 (Salmonella enterica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RALQTDIVAVQSQVVYGSVGNSIAVPAIKAQGLRVTAVPTVLFSNTPHYK
TFYGGIIPAEWFAGYLTALNERDALRELKAITTGYMGSADQIVLLSKWLM
AIRASHPEVCILVDPVIGDTDSGMYVQAEIPQAYRTHLLPQAQGLTPNVF
ELEMLSGKPCRTLEEAVAAAQSLLSTLKWVVITSAPGSLETITVAVTAQV
VEVFAHPRVATELKGTGDLFCAELVSGIVQGKKLTTAAKDAAQRVLEVMT
WTQQCGCDELILPP
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain5zwa Chain A Residue 309 [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]
PDB5zwa Structural and functional studies on Salmonella typhimurium pyridoxal kinase: the first structural evidence for the formation of Schiff base with the substrate.
Resolution2.45 Å
Binding residue
(original residue number in PDB)		N164 T200 S201 H225 R227 V228 T235 G236 V264 M268
Binding residue
(residue number reindexed from 1)		N148 T183 S184 H206 R208 V209 T216 G217 V245 M249
Annotation score5
Enzymatic activity
Enzyme Commision number 2.7.1.35: pyridoxal kinase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0008478 pyridoxal kinase activity
GO:0008902 hydroxymethylpyrimidine kinase activity
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0009443 pyridoxal 5'-phosphate salvage
GO:0016310 phosphorylation
GO:0042816 vitamin B6 metabolic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5zwa, PDBe:5zwa, PDBj:5zwa
PDBsum5zwa
PubMed31116912
UniProtA0A0F7J8S0

[Back to BioLiP]