Structure of PDB 3pgk Chain A Binding Site BS01

Receptor Information
>3pgk Chain A (length=415) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SLSSKLSVQDLDLKDKRVFIRVDFNVPLDGKKITSNQRIVAALPTIKYVL
EHHPRYVVLASHLGRPNGERNEKYSLAPVAKELQSLLGKDVTFLNDCVGP
EVEAAVKASAPGSVILLENLRYHIEEEGSRKVDGQKVKASKEDVQKFRHE
LSSLADVYINDAFGTAHRAHSSMVGFDLPQRAAGFLLEKELKYFGKALEN
PTRPFLAILGGAKVADKIQLIDNLLDKVDSIIIGGGMAFTFKKVLENTEI
GDSIFDKAVGPEIAKLMEKAKAKGVEVVLPVDFIIADAFSASANTKTVTD
KEGIPAGWQGLDNGPESRKLFAATVAKATVILWNGPPGVFEFEKFAAGTK
ALLDEVVKSSAAGNTVIIGGGDTATVAKKYGVTDKISHVSTGGGASLELL
EGKELPGVAFLSEKK
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 chain3pgk Chain A Residue 417 [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]
PDB3pgk Sequence and structure of yeast phosphoglycerate kinase.
Resolution2.5 Å
Binding residue
(original residue number in PDB)
G211 A212 K213 F289 L311 N334 G335 P336 G338 V339 D372
Binding residue
(residue number reindexed from 1)
G211 A212 K213 F289 L311 N334 G335 P336 G338 V339 D372
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) R38 K213 G371 G394
Catalytic site (residue number reindexed from 1) R38 K213 G371 G394
Enzyme Commision number 2.7.2.3: phosphoglycerate kinase.
Gene Ontology
Molecular Function
GO:0004618 phosphoglycerate kinase activity
Biological Process
GO:0006096 glycolytic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:3pgk, PDBe:3pgk, PDBj:3pgk
PDBsum3pgk
PubMed6765200
UniProtP00560|PGK_YEAST Phosphoglycerate kinase (Gene Name=PGK1)

[Back to BioLiP]