MolNFT v1 · #172076 · protein
Cryo-EM structure of trimeric prme spike of spondweni virus
6ZQJ · Genome polyprotein: “Cryo-EM structure of trimeric prme spike of spondweni virus”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.83). MolNFT v1 #172076 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6ZQJ
- 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 | 991 | 0.83 | 0.84 | 94 | empty |
| 2 | 540 | 0.75 | 0.82 | 55 | empty |
| 3 | 524 | 0.74 | 0.83 | 69 | empty |
| 4 | 688 | 0.74 | 0.80 | 74 | empty |
| 5 | 427 | 0.64 | 0.78 | 44 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1620 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1563 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 1558 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 413 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
- 6ZQJ · Cryo-EM structure of trimeric prME spike of 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 6ZQJ · PDBe 6ZQJ · UniProt C8XPB6
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