Research workbench
Cryoem structure of type II secretion system secretin gspd G453A mutant in vibrio cholerae
Analyse Cryoem structure of type II secretion system secretin gspd G453A mutant in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WQ9
- Type
- protein
- Length
- 7,395 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein D
- UniProt
- P45779
- Pockets
- 20 · best druggability 0.72
Structure
electron microscopy · 1 distinct chain · 28% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Type II secretion system protein D | protein | 493 | 28% helix, 40% strand | P45779 |
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 | 830 | 0.72 | 0.78 | 111 | empty |
| 2 | 421 | 0.69 | 0.81 | 53 | empty |
| 3 | 481 | 0.68 | 0.79 | 61 | empty |
| 4 | 488 | 0.68 | 0.79 | 56 | empty |
| 5 | 398 | 0.68 | 0.81 | 53 | empty |
Interfaces
30 interfaces between chains.
- I–J · 5692 Ų buried · 76 hydrogen bonds · protein-protein
- G–H · 5685 Ų buried · 76 hydrogen bonds · protein-protein
- K–L · 5685 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 5685 Ų buried · 76 hydrogen bonds · protein-protein
- B–C · 5683 Ų buried · 76 hydrogen bonds · protein-protein
Compared structures
- 5WQ9 · CryoEM structure of type II secretion system secretin GspD G453A mutant in Vibrio cholerae · the same entry in another collection · chain O against O, 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 P45779
- Elsewhere: RCSB PDB 5WQ9 · PDBe 5WQ9 · UniProt P45779
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