Research workbench
Cryo-EM structure of alphavirus M1
Analyse Cryo-EM structure of alphavirus M1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V4T
- Type
- protein
- Length
- 4,080 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E1 glycoprotein; E2 glycoprotein; Capsid protein
- UniProt
- A0MNM2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 11% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | E1 glycoprotein | protein | 437 | 11% helix, 30% strand | A0MNM2 |
| B, F, J, N | E2 glycoprotein | protein | 422 | 13% helix, 27% strand | A0MNM2 |
| C, G, K, O | Capsid protein | protein | 161 | 6% helix, 18% strand | A0MNM2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, E, F, I, J, M, N
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 | 924 | 0.82 | 0.84 | 93 | empty |
| 2 | 926 | 0.82 | 0.83 | 117 | empty |
| 3 | 652 | 0.81 | 0.86 | 97 | empty |
| 4 | 512 | 0.79 | 0.86 | 56 | empty |
| 5 | 427 | 0.78 | 0.86 | 64 | empty |
Interfaces
23 interfaces between chains.
- E–F · 3055 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 3046 Ų buried · 20 hydrogen bonds · protein-protein
- I–J · 2983 Ų buried · 20 hydrogen bonds · protein-protein
- M–N · 2966 Ų buried · 18 hydrogen bonds · protein-protein
- B–F · 682 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7V4T · Cryo-EM structure of Alphavirus M1 · 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 A0MNM2
- Elsewhere: RCSB PDB 7V4T · PDBe 7V4T · UniProt A0MNM2
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