Research workbench
Cryo-EM structure of an alphavirus, getah virus
Analyse Cryo-EM structure of an alphavirus, getah virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FD2
- Type
- protein
- Length
- 4,060 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Envelope glycoprotein 1; Envelope glycoprotein 2; Capsid protein
- EC
- 3.4.21.90
- UniProt
- A0A1Z2R994
- Ligands
- PLM, CLR, STE, PCW, NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I, M | Envelope glycoprotein 1 (EC 3.4.21.90) | protein | 438 | 10% helix, 41% strand | A0A1Z2R994 |
| B, F, J, N | Envelope glycoprotein 2 (EC 3.4.21.90) | protein | 419 | 16% helix, 38% strand | A0A1Z2R994 |
| C, G, K, O | Capsid protein (EC 3.4.21.90) | protein | 158 | 10% helix, 39% strand | A0A1Z2R994 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 12 copies · chains A, B, E, F, I, J, M, N
- CLR · Cholesterol · ligand · 12 copies · chains A, B, E, F, I, J, M, N
- STE · Stearic acid · ligand · 8 copies · chains A, B, E, F, I, J, M, N
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains A, B, E, F, I, J, M, N
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, E, F, I, J, M, N
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains A, E, I, M
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, E, I
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 | 1025 | 0.85 | 0.85 | 66 | empty |
| 2 | 789 | 0.84 | 0.87 | 73 | empty |
| 3 | 715 | 0.83 | 0.86 | 78 | empty |
| 4 | 724 | 0.81 | 0.84 | 89 | empty |
| 5 | 511 | 0.74 | 0.82 | 53 | empty |
Interfaces
24 interfaces between chains.
- A–B · 3440 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 3435 Ų buried · 27 hydrogen bonds · protein-protein
- I–J · 3433 Ų buried · 27 hydrogen bonds · protein-protein
- M–N · 3414 Ų buried · 23 hydrogen bonds · protein-protein
- E–M · 689 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 7FD2 · Cryo-EM structure of an alphavirus, Getah 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 A0A1Z2R994
- Elsewhere: RCSB PDB 7FD2 · PDBe 7FD2 · UniProt A0A1Z2R994
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