Research workbench
Crystal structure of LPG1832, a virk family protein from legionella pneumophila
Analyse Crystal structure of LPG1832, a virk family protein 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
- 5XTA
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virk protein
- UniProt
- A0A128ZU06
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Virk protein | protein | 120 | 13% helix, 53% strand | A0A128ZU06 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.85 | 0.89 | 45 | SO4, GOL |
| 2 | 439 | 0.75 | 0.84 | 39 | empty |
| 3 | 401 | 0.74 | 0.84 | 38 | empty |
| 4 | 383 | 0.74 | 0.84 | 39 | empty |
| 5 | 426 | 0.73 | 0.83 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–D · 920 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 916 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 896 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 26 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 3 disulfide (engineered, disulfide).
Compared structures
- 5XTA · Crystal structure of lpg1832, a VirK family protein from Legionella pneumophila · 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 A0A128ZU06
- Elsewhere: RCSB PDB 5XTA · PDBe 5XTA · UniProt A0A128ZU06
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.