Research workbench
8ZDS: Structure of the Salmonella flagellar MS-ring with C11 symmetry applied
Analyse 8ZDS: Structure of the Salmonella flagellar MS-ring with C11 symmetry applied in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8ZDS
- Type
- protein
- Length
- 9,053 residues
- Chains
- 33
- Method
- electron microscopy
- Authors
- Kinoshita, M., Makino, F., Miyata, T., Imada, K., Minamino, T., Namba, K.
- Deposited
- 05/03/24
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Salmonella enterica subsp. enterica serovar Typhimurium
- Molecule
- Flagellar M-ring protein
- UniProt
- P15928
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · resolution 3.1 · 2 distinct chains · 33% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, F, G, I, J, L, M, O, P, R, S, U, V, X, Y, a, b, d, e, g | Flagellar M-ring protein | protein | 257 | 32% helix, 34% strand | P15928 |
| B, E, H, K, N, Q, T, W, Z, c, f | Flagellar M-ring protein | protein | 309 | 34% helix, 29% strand | P15928 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.80 | 0.82 | 98 | empty |
| 2 | 649 | 0.77 | 0.82 | 66 | empty |
| 3 | 726 | 0.77 | 0.82 | 92 | empty |
| 4 | 713 | 0.77 | 0.82 | 94 | empty |
| 5 | 1134 | 0.77 | 0.79 | 111 | empty |
Interfaces
55 interfaces between chains.
- O–P · 3348 Ų buried · 45 hydrogen bonds · protein-protein
- U–V · 3343 Ų buried · 40 hydrogen bonds · protein-protein
- A–g · 3337 Ų buried · 43 hydrogen bonds · protein-protein
- L–M · 3333 Ų buried · 41 hydrogen bonds · protein-protein
- I–J · 3332 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- P15928 · AlphaFold monomer V2.0 prediction for flagellar M-ring protein (P15928) · a predicted model of the same protein · chain U against A, TM-score 0.70
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 P15928
- Elsewhere: RCSB PDB 8ZDS · PDBe 8ZDS · UniProt P15928
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