Research workbench
Cryo-EM structure of the T2SS secretin xcpq from pseudomonas aeruginosa
Analyse Cryo-EM structure of the T2SS secretin xcpq from pseudomonas aeruginosa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WLN
- Type
- protein
- Length
- 5,940 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein D
- UniProt
- P35818
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, O, A, B, C, D, E, F, H, I, J, K, L, M, N | Type II secretion system protein D | protein | 396 | 20% helix, 41% strand | P35818 |
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 | 1113 | 0.79 | 0.81 | 101 | empty |
| 2 | 352 | 0.76 | 0.86 | 66 | empty |
| 3 | 519 | 0.75 | 0.83 | 67 | empty |
| 4 | 752 | 0.75 | 0.80 | 96 | empty |
| 5 | 1146 | 0.74 | 0.77 | 129 | empty |
Interfaces
30 interfaces between chains.
- C–D · 4948 Ų buried · 68 hydrogen bonds · protein-protein
- E–F · 4906 Ų buried · 62 hydrogen bonds · protein-protein
- O–N · 4895 Ų buried · 53 hydrogen bonds · protein-protein
- G–H · 4842 Ų buried · 53 hydrogen bonds · protein-protein
- I–J · 4755 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 5WLN · Cryo-EM structure of the T2SS secretin XcpQ from Pseudomonas aeruginosa · the same entry in another collection · chain N against N, 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 P35818
- Elsewhere: RCSB PDB 5WLN · PDBe 5WLN · UniProt P35818
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.