Research workbench
Cryo-EM structure of the mature and infective mayaro virus
Analyse Cryo-EM structure of the mature and infective mayaro virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KO8
- Type
- protein
- Length
- 4,004 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; E1 glycoprotein; E2 glycoprotein
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 8% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Capsid protein | protein | 152 | 0% helix, 36% strand | — |
| B, E, H, L | E1 glycoprotein | protein | 433 | 7% helix, 35% strand | — |
| C, F, I, M | E2 glycoprotein | protein | 416 | 11% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains B, C, E, F, H, L, M, I
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains L
- BMA · beta-D-mannopyranose · sugar · 7 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 925 | 0.85 | 0.87 | 107 | empty |
| 2 | 706 | 0.82 | 0.86 | 84 | empty |
| 3 | 683 | 0.82 | 0.86 | 76 | empty |
| 4 | 1134 | 0.81 | 0.82 | 104 | empty |
| 5 | 411 | 0.80 | 0.88 | 56 | empty |
Interfaces
26 interfaces between chains.
- E–F · 3068 Ų buried · 21 hydrogen bonds · protein-protein
- L–M · 3050 Ų buried · 16 hydrogen bonds · protein-protein
- H–I · 2922 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 2847 Ų buried · 21 hydrogen bonds · protein-protein
- H–L · 620 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 7KO8 · Cryo-EM structure of the mature and infective Mayaro virus · the same entry in another collection · chain E against E, 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
- Elsewhere: RCSB PDB 7KO8 · PDBe 7KO8
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