Research workbench
Crystal structure of VP5 from haloarchaeal pleomorphic virus 2
Analyse Crystal structure of VP5 from haloarchaeal pleomorphic virus 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QGI
- Type
- protein
- Length
- 498 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP5
- UniProt
- H9ABL9
- Ligands
- NAG, CL
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP5 | protein | 498 | 35% helix, 26% strand | H9ABL9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CL · Chloride ion · ion · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.43 | 0.83 | 14 | empty |
| 2 | 56 | 0.35 | 0.79 | 15 | empty |
Modifications
Observed in the structure: 1 glycan (N-glycosylation).
Compared structures
- 6QGI · Crystal structure of VP5 from Haloarchaeal pleomorphic virus 2 · 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 H9ABL9
- Elsewhere: RCSB PDB 6QGI · PDBe 6QGI · UniProt H9ABL9
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