Research workbench
Crystal structure of an antigenic outer membrane protein ST50 from salmonella typhi
Analyse Crystal structure of an antigenic outer membrane protein ST50 from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BUN
- Type
- protein
- Length
- 1,285 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein
- Pockets
- 14 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein | protein | 427 | 65% helix, 12% strand | — |
| B | Outer membrane protein | protein | 425 | 64% helix, 14% strand | — |
| C | Outer membrane protein | protein | 433 | 63% helix, 12% strand | — |
Ligands and binding sites
- BOG · octyl beta-D-glucopyranoside · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 810 | 0.73 | 0.78 | 105 | BOG |
| 2 | 172 | 0.50 | 0.77 | 23 | empty |
| 3 | 174 | 0.49 | 0.77 | 34 | empty |
| 4 | 149 | 0.45 | 0.76 | 24 | empty |
| 5 | 132 | 0.43 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2606 Ų buried · 53 hydrogen bonds · protein-protein
- A–C · 2587 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 2575 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 5BUN · Crystal structure of an antigenic outer membrane protein ST50 from Salmonella Typhi · 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
- Elsewhere: RCSB PDB 5BUN · PDBe 5BUN
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