Research workbench
Cryo-EM structure of spondweni virus prme
Analyse Cryo-EM structure of spondweni virus prme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZQI
- Type
- protein
- Length
- 655 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- C8XPB6
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.74
Structure
electron microscopy · 3 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 504 | 19% helix, 36% strand | C8XPB6 |
| B | Genome polyprotein | protein | 101 | 0% helix, 34% strand | C8XPB6 |
| C | Genome polyprotein | protein | 50 | 72% helix, 0% strand | C8XPB6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 521 | 0.74 | 0.82 | 52 | empty |
| 2 | 323 | 0.60 | 0.78 | 51 | empty |
| 3 | 62 | 0.42 | 0.81 | 21 | empty |
| 4 | 71 | 0.40 | 0.79 | 16 | empty |
| 5 | 69 | 0.37 | 0.78 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1627 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 367 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZQI · Cryo-EM structure of Spondweni virus prME · 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
- Elsewhere: RCSB PDB 6ZQI · PDBe 6ZQI · UniProt C8XPB6
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