MolNFT v1 · #17032 · protein
The structure of bacillus subtilis rbsd complexed with ribose 5- phosphate
1OGE · High affinity ribose transport protein rbsd: “The structure of bacillus subtilis rbsd complexed with ribose 5- phosphate”. X-ray diffraction, 2 ligands (RP5, CL), 20 pockets (best druggability 0.52). MolNFT v1 #17032 on GenesisL1…
- PDB
- 1OGE
- Type
- protein
- Length
- 655 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- High affinity ribose transport protein rbsd
- UniProt
- P36946
- Ligands
- RP5, CL
- Pockets
- 20 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | High affinity ribose transport protein rbsd | protein | 131 | 34% helix, 23% strand | P36946 |
Ligands and binding sites
- RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · 5 copies · chains A, E, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.52 | 0.79 | 20 | empty |
| 2 | 184 | 0.52 | 0.78 | 25 | empty |
| 3 | 173 | 0.51 | 0.77 | 26 | empty |
| 4 | 187 | 0.50 | 0.77 | 28 | empty |
| 5 | 158 | 0.49 | 0.77 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 411 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 408 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 405 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 403 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 401 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1OGE · The Structure of Bacillus subtilis RbsD complexed with Ribose 5-phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P36946 · AlphaFold monomer V2.0 prediction for D-ribose pyranase (P36946) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P36946
- Elsewhere: RCSB PDB 1OGE · PDBe 1OGE · UniProt P36946
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