Research workbench
Cryo-EM structure of the flagellar lp ring from salmonella
Analyse Cryo-EM structure of the flagellar lp ring from salmonella in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CBL
- Type
- protein
- Length
- 13,364 residues
- Chains
- 52
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flagellar L-ring protein; Flagellar P-ring protein
- UniProt
- P0A1N8, P15930
- Ligands
- OCA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 18% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z | Flagellar L-ring protein | protein | 211 | 14% helix, 45% strand | P0A1N8 |
| a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x, y, z | Flagellar P-ring protein | protein | 303 | 22% helix, 31% strand | P15930 |
Ligands and binding sites
- OCA · Octanoic acid (caprylic acid) · ligand · 26 copies · chains A, Y, Z, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1004 | 0.88 | 0.90 | 142 | empty |
| 2 | 1063 | 0.88 | 0.89 | 125 | empty |
| 3 | 728 | 0.86 | 0.90 | 108 | empty |
| 4 | 769 | 0.86 | 0.90 | 105 | empty |
| 5 | 750 | 0.86 | 0.89 | 103 | empty |
Interfaces
260 interfaces between chains.
- y–z · 3521 Ų buried · 40 hydrogen bonds · protein-protein
- q–r · 3480 Ų buried · 45 hydrogen bonds · protein-protein
- k–l · 3480 Ų buried · 39 hydrogen bonds · protein-protein
- u–v · 3479 Ų buried · 41 hydrogen bonds · protein-protein
- x–y · 3478 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 covalent, 26 disulfide (covalent ligand, disulfide).
Compared structures
- 7CBL · Cryo-EM structure of the flagellar LP ring from Salmonella · the same entry in another collection · chain F against F, 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 P0A1N8
- Every structure of UniProt P15930
- Elsewhere: RCSB PDB 7CBL · PDBe 7CBL · UniProt P0A1N8 · UniProt P15930
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