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The crystal structure of an effector protein vipe from legionella pneumophila subsp. pneumophila str. philadelphia 1
Analyse The crystal structure of an effector protein vipe from legionella pneumophila… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QN8
- Type
- protein
- Length
- 455 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vipe
- UniProt
- Q5ZRR7
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Vipe | protein | 153 | 64% helix, 1% strand | Q5ZRR7 |
| C | Vipe | protein | 149 | 66% helix, 1% strand | Q5ZRR7 |
Ligands and binding sites
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.67 | 0.79 | 55 | empty |
| 2 | 125 | 0.52 | 0.81 | 26 | empty |
| 3 | 84 | 0.42 | 0.79 | 25 | empty |
| 4 | 88 | 0.40 | 0.78 | 24 | empty |
| 5 | 64 | 0.37 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 794 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 767 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 138 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 4QN8 · The crystal structure of an effector protein VipE from Legionella pneumophila subsp.… · 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 Q5ZRR7
- Elsewhere: RCSB PDB 4QN8 · PDBe 4QN8 · UniProt Q5ZRR7
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