Structure of PDB 3i3y Chain D Binding Site BS01

Receptor Information
>3i3y Chain D (length=285) Species: 272620 (Klebsiella pneumoniae subsp. pneumoniae MGH 78578) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LRVYVTGNITVDETWSIPDIPKKGASIHGVKVSQDIGGKGANQAIILSRC
GIETRLIAATGNDSNGAWIRQQIKNEPLMLLPDGHFNQHSDTSIILNSAD
GDNAIITTTAAADTFSLDEMIPHMADAVAGDILLQQGNFSLDKTRALFQY
ARSRGMTTVFNPSPVNPDFCHLWPLIDIAVVNESEAELLQPYGVKTLVIT
QGAAGAWLVQEGQRQFCPAVPAEALDTTGAGDTFLAVMLASALLRGVAPD
ALALAHASRAAAITVSRRGTLSAFPGSRELAALLT
Ligand information
Ligand IDRIB
InChIInChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5+/m1/s1
InChIKeyHMFHBZSHGGEWLO-AIHAYLRMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C(C1C(C(C(O1)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0C([C@@H]1[C@H]([C@H]([C@H](O1)O)O)O)O
ACDLabs 10.04OC1C(OC(O)C1O)CO
FormulaC5 H10 O5
Namealpha-D-ribofuranose;
alpha-D-ribose;
D-ribose;
ribose
ChEMBLCHEMBL606078
DrugBank
ZINCZINC000003860714
PDB chain3i3y Chain D Residue 311 [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]
PDB3i3y Crystal structure of Ribokinase in Complex with D-Ribose from Klebsiella pneumoniae
Resolution2.15 Å
Binding residue
(original residue number in PDB)		D12 G37 G38 K39 N42 S93 D232
Binding residue
(residue number reindexed from 1)		D12 G37 G38 K39 N42 S93 D232
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) G229 A230 G231 D232
Catalytic site (residue number reindexed from 1) G229 A230 G231 D232
Enzyme Commision number 2.7.1.15: ribokinase.
Gene Ontology
Molecular Function
GO:0004747 ribokinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0046872 metal ion binding
Biological Process
GO:0006014 D-ribose metabolic process
GO:0016310 phosphorylation
GO:0019303 D-ribose catabolic process
GO:0046835 carbohydrate phosphorylation
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3i3y, PDBe:3i3y, PDBj:3i3y
PDBsum3i3y
PubMed
UniProtA6T989

[Back to BioLiP]