Structure of PDB 1oge Chain D Binding Site BS01

Receptor Information

>1oge Chain D (length=131) Species: 1423 (Bacillus subtilis)

MKKHGILNSHLAKILADLGHTDKIVIADAGLPVPDGVLKIDLSLKPGLPA
FQDTAAVLAEEMAVEKVIAAAEIKASNQENAKFLENLFSEQEIEYLSHEE
FKLLTKDAKAVIRTGEFTPYANCILQAGVLF

Ligand information

• Ligand ID: RP5
• InChI: InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5-/m1/s1
• InChIKey: KTVPXOYAKDPRHY-TXICZTDVSA-N
• SMILES:
  CACTVS 3.370: O[CH]1O[CH](CO[P](O)(O)=O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.7.0: C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)OP(=O)(O)O
  OpenEye OEToolkits 1.7.0: C(C1C(C(C(O1)O)O)O)OP(=O)(O)O
  CACTVS 3.370: O[C@@H]1O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]1O
  ACDLabs 12.01: O=P(O)(O)OCC1OC(O)C(O)C1O
• Formula: C5 H11 O8 P
• Name: 5-O-phosphono-beta-D-ribofuranose;
  [(2R,3S,4S,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN PHOSPHATE;
  5-O-phosphono-beta-D-ribose;
  5-O-phosphono-D-ribose;
  5-O-phosphono-ribose
• ChEMBL: CHEMBL1235722
• DrugBank: DB04352
• ZINC: ZINC000004228241
• PDB chain: 1oge Chain D Residue 1133

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1oge Crystal Structures of Rbsd Leading to the Identification of Cytoplasmic Sugar-Binding Proteins with a Novel Folding Architecture
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): D28 G30 L31 H98 Y120
• Binding residue (residue number reindexed from 1): D28 G30 L31 H98 Y120
• Annotation score: 2

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

External links

• PDB: RCSB:1oge, PDBe:1oge, PDBj:1oge
• PDBsum: 1oge
• PubMed: 12738765
• UniProt: P36946|RBSD_BACSU D-ribose pyranase (Gene Name=rbsD)