Structure of PDB 1kc7 Chain A Binding Site BS02

Receptor Information
>1kc7 Chain A (length=872) Species: 1512 ([Clostridium] symbiosum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AKWVYKFEEGNASMRNLLGGKGCNLAEMTILGMPIPQGFTVTTEACTEYY
NSGKQITQEIQDQIFEAITWLEELNGKKFGDTEDPLLVSVRSGARASMPG
MMDTILNLGLNDVAVEGFAKKTGNPRFAYDSYRRFIQMYSDVVMEVPKSH
FEKIIDAMKEEKGVHFDTDLTADDLKELAEKFKAVYKEAMNGEEFPQEPK
DQLMGAVKAVFRSWDNPRAIVYRRMNDIPGDWGTAVNVQTMVFGNKGETS
GTGVAFTRNPSTGEKGIYGEYLINAQGEDVVAGVRTPQPITQLENDMPDC
YKQFMDLAMKLEKHFRDMQDMEFTIEEGKLYFLQTRNGKRTAPAALQIAC
DLVDEGMITEEEAVVRIEAKSLDQLLHPTFNPAALKAGEVIGSALPASPG
AAAGKVYFTADEAKAAHEKGERVILVRLETSPEDIEGMHAAEGILTVRGG
MTSHAAVVARGMGTCCVSGCGEIKINEEAKTFELGGHTFAEGDYISLDGS
TGKIYKGDIETQEASVSGSFERIMVWADKFRTLKVRTNADTPEDTLNAVK
LGAEGIGLCRTEHMFFEADRIMKIRKMILSDSVEAREEALNELIPFQKGD
FKAMYKALEGRPMTVRYLDPPLHEFVPHTEEEQAELAKNMGLTLAEVKAK
VDELHEFNPMMGHRGCRLAVTYPEIAKMQTRAVMEAAIEVKEETGIDIVP
EIMIPLVGEKKELKFVKDVVVEVAEQVKKEKGSDMQYHIGTMIEIPRAAL
TADAIAEEAEFFSFGTNDLTQMTFGFSRDDAGKFLDSYYKAKIYESDPFA
RLDQTGVGQLVEMAVKKGRQTRPGLKCGICGEHGGDPSSVEFCHKVGLNY
VSCSPFRVPIARLAAAQAALNN
Ligand information
Ligand IDPPR
InChIInChI=1S/C3H5O6P/c4-2(3(5)6)1-10(7,8)9/h1H2,(H,5,6)(H2,7,8,9)
InChIKeyCHDDAVCOAOFSLD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C(=O)CP(=O)(O)O
CACTVS 3.341OC(=O)C(=O)C[P](O)(O)=O
OpenEye OEToolkits 1.5.0C(C(=O)C(=O)O)P(=O)(O)O
FormulaC3 H5 O6 P
NamePHOSPHONOPYRUVATE
ChEMBL
DrugBankDB02522
ZINCZINC000004095926
PDB chain1kc7 Chain A Residue 1000 [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]
PDB1kc7 Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R561 R617 E745 G766 T767 N768 D769
Binding residue
(residue number reindexed from 1)		R560 R616 E744 G765 T766 N767 D768
Annotation score1
Binding affinityMOAD: Ki=3uM
PDBbind-CN: -logKd/Ki=5.52,Ki=3uM
Enzymatic activity
Catalytic site (original residue number in PDB) K22 R92 G101 M103 R337 H455 E745 S764 D769 C831 Y851
Catalytic site (residue number reindexed from 1) K21 R91 G100 M102 R336 H454 E744 S763 D768 C830 Y850
Enzyme Commision number 2.7.9.1: pyruvate, phosphate dikinase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016772 transferase activity, transferring phosphorus-containing groups
GO:0046872 metal ion binding
GO:0050242 pyruvate, phosphate dikinase activity
Biological Process
GO:0006090 pyruvate metabolic process
GO:0016310 phosphorylation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1kc7, PDBe:1kc7, PDBj:1kc7
PDBsum1kc7
PubMed11790099
UniProtP22983|PPDK_CLOSY Pyruvate, phosphate dikinase (Gene Name=ppdK)

[Back to BioLiP]