Research workbench
Fitting result in the O-layer of the subnanometer structure of the bacterial PKM101 type IV secretion system core complex digested with elastase
Analyse Fitting result in the O-layer of the subnanometer structure of the bacterial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZBI
- Type
- protein
- Length
- 4,956 residues
- Chains
- 42
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Traf protein; Trao protein; Tran protein
- UniProt
- Q46705, Q46704, Q46702
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 3 distinct chains · 14% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J, M, P, S, V, Y, b, e, h, k, n | Traf protein | protein | 196 | 18% helix, 19% strand | Q46705 |
| B, E, H, K, N, Q, T, W, Z, c, f, i, l, o | Trao protein | protein | 130 | 12% helix, 25% strand | Q46704 |
| C, F, I, L, O, R, U, X, a, d, g, j, m, p | Tran protein | protein | 28 | 0% helix, 4% strand | Q46702 |
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 | 433 | 0.74 | 0.84 | 66 | empty |
| 2 | 434 | 0.73 | 0.83 | 64 | empty |
| 3 | 411 | 0.73 | 0.84 | 64 | empty |
| 4 | 430 | 0.73 | 0.83 | 71 | empty |
| 5 | 396 | 0.73 | 0.84 | 64 | empty |
Interfaces
126 interfaces between chains.
- J–M · 2254 Ų buried · 29 hydrogen bonds · protein-protein
- b–e · 2254 Ų buried · 29 hydrogen bonds · protein-protein
- D–G · 2252 Ų buried · 29 hydrogen bonds · protein-protein
- Y–b · 2250 Ų buried · 29 hydrogen bonds · protein-protein
- P–S · 2250 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 3ZBI · Fitting result in the O-layer of the subnanometer structure of the bacterial pKM101 type… · the same entry in another collection · chain D against D, 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 Q46705
- Every structure of UniProt Q46704
- Every structure of UniProt Q46702
- Elsewhere: RCSB PDB 3ZBI · PDBe 3ZBI · UniProt Q46705 · UniProt Q46704 · UniProt Q46702
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