Structure of PDB 3k56 Chain A Binding Site BS01

Receptor Information
>3k56 Chain A (length=260) Species: 2190 (Methanocaldococcus jannaschii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLTILKLGGSILSDKNVPYSIKWDNLERIAMEIKNALDYYKNQNKEIKLI
LVHGGGAFGHPVAKKYLKIEDGKKIFINMEKGFWEIQRAMRRFNNIIIDT
LQSYDIPAVSIQPSSFVVFGDKLIFDTSAIKEMLKRNLVPVIHGDIVIDD
KNGYRIISGDDIVPYLANELKADLILYATDVDGVLIDNKPIKRIDKNNIY
KILNYLSGSNSIDVTGGMKYKIEMIRKNKCRGFVFNGNKANNIYKALLGE
VEGTEIDFSE
Ligand information
Ligand IDIS3
InChIInChI=1S/C5H14O6P2S/c1-5(2)3-4-10-12(6,7)11-13(8,9)14/h5H,3-4H2,1-2H3,(H,6,7)(H2,8,9,14)
InChIKeyJPPCYMVZXKAWTF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 11.02O=P(O)(OP(=O)(OCCC(C)C)O)S
CACTVS 3.352CC(C)CCO[P](O)(=O)O[P](O)(S)=O
OpenEye OEToolkits 1.7.0CC(C)CCOP(=O)(O)OP(=O)(O)S
OpenEye OEToolkits 1.7.0CC(C)CCO[P@@](=O)(O)O[P@](=O)(O)S
FormulaC5 H14 O6 P2 S
NameIsopentenyl Diphosphate Beta-S;
O-(3-methylbutyl) trihydrogen thiodiphosphate
ChEMBL
DrugBank
ZINC
PDB chain3k56 Chain A Residue 300 [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]
PDB3k56 Mutation of archaeal isopentenyl phosphate kinase highlights mechanism and guides phosphorylation of additional isoprenoid monophosphates.
Resolution2.34 Å
Binding residue
(original residue number in PDB)		G9 G54 G55 G56 G59 H60 G144 I156 S158 G159
Binding residue
(residue number reindexed from 1)		G9 G54 G55 G56 G59 H60 G144 I156 S158 G159
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.4.26: isopentenyl phosphate kinase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0102043 isopentenyl phosphate kinase activity
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0016310 phosphorylation
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3k56, PDBe:3k56, PDBj:3k56
PDBsum3k56
PubMed20392112
UniProtQ60352|IPK_METJA Isopentenyl phosphate kinase (Gene Name=MJ0044)

[Back to BioLiP]