Research workbench
V. cholera biofilm scaffolding protein rbma in complex with 18-crown-6
Analyse V. cholera biofilm scaffolding protein rbma in complex with 18-crown-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BEI
- Type
- protein
- Length
- 1,866 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rbma
- UniProt
- C3NSJ9
- Ligands
- O4B
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G | Rbma | protein | 233 | 0% helix, 60% strand | C3NSJ9 |
| D, H | Rbma | protein | 234 | 0% helix, 59% strand | C3NSJ9 |
Ligands and binding sites
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.84 | 0.86 | 114 | O4B |
| 2 | 1018 | 0.84 | 0.85 | 116 | O4B |
| 3 | 1042 | 0.81 | 0.82 | 101 | O4B |
| 4 | 1093 | 0.80 | 0.82 | 108 | O4B |
| 5 | 338 | 0.67 | 0.81 | 40 | empty |
Interfaces
13 interfaces between chains.
- C–D · 2961 Ų buried · 48 hydrogen bonds · protein-protein
- E–F · 2954 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2947 Ų buried · 46 hydrogen bonds · protein-protein
- G–H · 2934 Ų buried · 46 hydrogen bonds · protein-protein
- A–F · 429 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4BEI · V. cholera biofilm scaffolding protein RbmA in complex with 18-crown- 6 · the same entry in another collection · chain A against A, TM-score 1.00
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 C3NSJ9
- Elsewhere: RCSB PDB 4BEI · PDBe 4BEI · UniProt C3NSJ9
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