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The structure of bacillus subtilis rbsd complexed with glycerol
Analyse The structure of bacillus subtilis rbsd complexed with glycerol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OGF
- 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
- CL
- Pockets
- 19 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | High affinity ribose transport protein rbsd | protein | 131 | 34% helix, 24% strand | P36946 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 166 | 0.52 | 0.78 | 27 | empty |
| 2 | 161 | 0.51 | 0.78 | 23 | empty |
| 3 | 171 | 0.51 | 0.78 | 29 | CL |
| 4 | 167 | 0.49 | 0.77 | 30 | empty |
| 5 | 144 | 0.48 | 0.78 | 24 | empty |
Interfaces
5 interfaces between chains.
- B–C · 440 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 435 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 432 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 428 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 426 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
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 1OGF · PDBe 1OGF · UniProt P36946
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