Research workbench
O-layer structure (TRWH/VIRB7, TRWF/VIRB9CTD, TRWE/VIRB10CTD) of the outer membrane core complex from the fully-assembled R388 type IV secretion system determined by cryo-EM.
Analyse O-layer structure (TRWH/VIRB7, TRWF/VIRB9CTD, TRWE/VIRB10CTD) of the outer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O3J
- Type
- protein
- Length
- 5,054 residues
- Chains
- 42
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trwe protein; Trwf protein; Trwh protein
- UniProt
- O50337, O50336, O50334
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 3 distinct chains · 15% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V, Y, b, e, h, k, n | Trwe protein | protein | 202 | 19% helix, 36% strand | O50337 |
| B, E, H, K, N, Q, T, W, Z, c, f, i, l, o | Trwf protein | protein | 131 | 13% helix, 37% strand | O50336 |
| C, F, I, L, O, R, U, X, a, d, g, j, m, p | Trwh protein | protein | 28 | 0% helix, 7% strand | O50334 |
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 | 150 | 0.79 | 0.96 | 34 | empty |
| 2 | 138 | 0.79 | 0.96 | 31 | empty |
| 3 | 136 | 0.79 | 0.97 | 32 | empty |
| 4 | 139 | 0.78 | 0.96 | 31 | empty |
| 5 | 134 | 0.78 | 0.96 | 31 | empty |
Interfaces
140 interfaces between chains.
- V–Y · 2348 Ų buried · 28 hydrogen bonds · protein-protein
- b–e · 2342 Ų buried · 28 hydrogen bonds · protein-protein
- A–n · 2337 Ų buried · 29 hydrogen bonds · protein-protein
- P–S · 2336 Ų buried · 28 hydrogen bonds · protein-protein
- G–J · 2335 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 7O3J · O-layer structure (TrwH/VirB7, TrwF/VirB9CTD, TrwE/VirB10CTD) of the outer membrane core… · the same entry in another collection · chain B against B, 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 O50337
- Every structure of UniProt O50336
- Every structure of UniProt O50334
- Elsewhere: RCSB PDB 7O3J · PDBe 7O3J · UniProt O50337 · UniProt O50336 · UniProt O50334
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