Research workbench
Crystal structure of the legionella effector wipa
Analyse Crystal structure of the legionella effector wipa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N6X
- Type
- protein
- Length
- 796 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wipa
- UniProt
- Q5GA16
- Ligands
- MN, BR, PO4
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wipa | protein | 396 | 56% helix, 12% strand | Q5GA16 |
| B | Wipa | protein | 400 | 55% helix, 12% strand | Q5GA16 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- BR · Bromide ion · ion · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.60 | 0.81 | 29 | empty |
| 2 | 161 | 0.57 | 0.82 | 26 | empty |
| 3 | 83 | 0.55 | 0.85 | 16 | MPD |
| 4 | 88 | 0.54 | 0.84 | 15 | MPD |
| 5 | 123 | 0.52 | 0.82 | 27 | MN, PO4 |
Interfaces
1 interface between chains.
- A–B · 1155 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5N6X · Crystal structure of the Legionella effector WipA · the same entry in another collection · chain A against A, 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 Q5GA16
- Elsewhere: RCSB PDB 5N6X · PDBe 5N6X · UniProt Q5GA16
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