Research workbench
Cryo-EM structure of mature spondweni virus
Analyse Cryo-EM structure of mature spondweni virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZQV
- Type
- protein
- Length
- 1,734 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- C8XPB6, A0A2L1GGB4
- Ligands
- 3PE, NAG, FUC
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Genome polyprotein | protein | 504 | 21% helix, 39% strand | C8XPB6 |
| B, D, F | Genome polyprotein | protein | 74 | 58% helix, 0% strand | A0A2L1GGB4 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 3 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.88 | 0.89 | 119 | empty |
| 2 | 1155 | 0.73 | 0.77 | 96 | 3PE |
| 3 | 624 | 0.68 | 0.77 | 71 | empty |
| 4 | 421 | 0.65 | 0.79 | 64 | empty |
| 5 | 110 | 0.61 | 0.87 | 19 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1778 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1771 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1750 Ų buried · 17 hydrogen bonds · protein-protein
- C–E · 1581 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1147 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZQV · Cryo-EM structure of mature Spondweni virus · 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 C8XPB6
- Every structure of UniProt A0A2L1GGB4
- Elsewhere: RCSB PDB 6ZQV · PDBe 6ZQV · UniProt C8XPB6 · UniProt A0A2L1GGB4
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