Research workbench
Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri
Analyse Cryo-EM structure of the bacteria-killing type IV secretion system core complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GYB
- Type
- protein
- Length
- 7,546 residues
- Chains
- 42
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.28
- Source
- Xanthomonas axonopodis pv. citri (strain 306)
- Molecule
- VirB7; VirB9 protein; VirB10 protein
- UniProt
- Q8PJB3, Q8PJB5, Q8PJB6
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · resolution 3.28 · 3 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, d, g, j, m, p, s, A, D, G, J, M, P, S | VirB7 | protein | 111 | 22% helix, 26% strand | Q8PJB3 |
| b, e, h, k, n, q, t, B, E, H, K, N, Q, T | VirB9 protein | protein | 223 | 6% helix, 43% strand | Q8PJB5 |
| c, f, i, l, o, r, u, C, F, I, L, O, R, U | VirB10 protein | protein | 205 | 24% helix, 30% strand | Q8PJB6 |
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 | 127 | 0.77 | 0.95 | 34 | empty |
| 2 | 119 | 0.77 | 0.96 | 36 | empty |
| 3 | 109 | 0.77 | 0.96 | 37 | empty |
| 4 | 121 | 0.76 | 0.96 | 38 | empty |
| 5 | 114 | 0.76 | 0.96 | 36 | empty |
Interfaces
140 interfaces between chains.
- i–l · 2377 Ų buried · 25 hydrogen bonds · protein-protein
- l–o · 2376 Ų buried · 26 hydrogen bonds · protein-protein
- I–L · 2376 Ų buried · 25 hydrogen bonds · protein-protein
- o–r · 2375 Ų buried · 25 hydrogen bonds · protein-protein
- O–R · 2374 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 6GYB · Cryo-EM structure of the bacteria-killing type IV secretion system core complex from… · 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 Q8PJB3
- Every structure of UniProt Q8PJB5
- Every structure of UniProt Q8PJB6
- Elsewhere: RCSB PDB 6GYB · PDBe 6GYB · UniProt Q8PJB3 · UniProt Q8PJB5 · UniProt Q8PJB6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.