Structure of PDB 1ogd Chain C Binding Site BS01

Receptor Information
>1ogd Chain C (length=131) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPA
FQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEE
FKLLTKDAKAVIRTGEFTPYANCILQAGVLF
Ligand information
Ligand IDRIP
InChIInChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4-,5-/m1/s1
InChIKeySRBFZHDQGSBBOR-TXICZTDVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1C(C(C(C(O1)O)O)O)O
OpenEye OEToolkits 1.5.0C1[C@H]([C@H]([C@H]([C@@H](O1)O)O)O)O
CACTVS 3.341O[CH]1CO[CH](O)[CH](O)[CH]1O
CACTVS 3.341O[C@@H]1CO[C@@H](O)[C@H](O)[C@@H]1O
ACDLabs 10.04OC1C(O)COC(O)C1O
FormulaC5 H10 O5
Namebeta-D-ribopyranose;
beta-D-ribose;
D-ribose;
ribose;
RIBOSE(PYRANOSE FORM)
ChEMBLCHEMBL1159662
DrugBankDB04286
ZINCZINC000004097544
PDB chain1ogd Chain C Residue 1132 [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]
PDB1ogd Crystal Structures of Rbsd Leading to the Identification of Cytoplasmic Sugar-Binding Proteins with a Novel Folding Architecture
Resolution1.95 Å
Binding residue
(original residue number in PDB)		D28 G30 L31 Y120
Binding residue
(residue number reindexed from 1)		D28 G30 L31 Y120
Annotation score5
Binding affinityMOAD: Kd=0.93mM
Enzymatic activity
Enzyme Commision number 5.4.99.62: D-ribose pyranase.
Gene Ontology
Molecular Function
GO:0016853 isomerase activity
GO:0016866 intramolecular transferase activity
GO:0016872 intramolecular lyase activity
GO:0048029 monosaccharide binding
GO:0062193 D-ribose pyranase activity
Biological Process
GO:0005996 monosaccharide metabolic process
GO:0019303 D-ribose catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ogd, PDBe:1ogd, PDBj:1ogd
PDBsum1ogd
PubMed12738765
UniProtP36946|RBSD_BACSU D-ribose pyranase (Gene Name=rbsD)

[Back to BioLiP]