Research workbench
Structure of the outer-membrane core complex (inner ring) from a conjugative type IV secretion system
Analyse Structure of the outer-membrane core complex (inner ring) from a conjugative… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OKN
- Type
- protein
- Length
- 3,757 residues
- Chains
- 34
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trab; Type IV conjugative transfer system lipoprotein trav
- UniProt
- A0A753A8N9
- Pockets
- 20 · best druggability 0.67
Structure
electron microscopy · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K, M, O, Q, S, U, W, Y, a, c, e, g | Trab | protein | 183 | 21% helix, 35% strand | — |
| B, D, F, H, J, L, N, P, R, T, V, X, Z, b, d, f, h | Type IV conjugative transfer system lipoprotein trav | protein | 38 | 42% helix, 0% strand | A0A753A8N9 |
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 | 590 | 0.67 | 0.77 | 86 | empty |
| 2 | 403 | 0.65 | 0.79 | 57 | empty |
| 3 | 512 | 0.65 | 0.77 | 72 | empty |
| 4 | 363 | 0.63 | 0.79 | 48 | empty |
| 5 | 367 | 0.63 | 0.79 | 51 | empty |
Interfaces
102 interfaces between chains.
- A–E · 1677 Ų buried · 23 hydrogen bonds · protein-protein
- K–M · 1635 Ų buried · 16 hydrogen bonds · protein-protein
- S–U · 1634 Ų buried · 16 hydrogen bonds · protein-protein
- C–G · 1632 Ų buried · 16 hydrogen bonds · protein-protein
- E–I · 1631 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide (disulfide).
Compared structures
- 7OKN · Structure of the outer-membrane core complex (inner ring) from a conjugative type IV… · 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 A0A753A8N9
- Elsewhere: RCSB PDB 7OKN · PDBe 7OKN · UniProt A0A753A8N9
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