MolNFT v1 · #172088 · protein
Cryo-EM structure of immature spondweni virus
6ZQW · Genome polyprotein: “Cryo-EM structure of immature spondweni virus”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #172088 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZQW
- Type
- protein
- Length
- 1,965 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Prm
- UniProt
- C8XPB6
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Genome polyprotein | protein | 504 | 19% helix, 35% strand | C8XPB6 |
| B, E, H | Prm | protein | 101 | 0% helix, 34% strand | C8XPB6 |
| I, F, C | Prm | protein | 50 | 72% helix, 0% strand | C8XPB6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.83 | 0.84 | 93 | empty |
| 2 | 673 | 0.75 | 0.81 | 73 | empty |
| 3 | 545 | 0.74 | 0.82 | 63 | empty |
| 4 | 543 | 0.74 | 0.82 | 59 | empty |
| 5 | 447 | 0.63 | 0.77 | 49 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1614 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1563 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1554 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 414 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 390 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZQW · Cryo-EM structure of immature 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
- Elsewhere: RCSB PDB 6ZQW · PDBe 6ZQW · UniProt C8XPB6
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