Research workbench
CryoEM structure of chimeric Eastern Equine Encephalitis Virus
Analyse CryoEM structure of chimeric Eastern Equine Encephalitis Virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MX4
- Type
- protein
- Length
- 4,039 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.4
- Source
- Eastern equine encephalitis virus
- Molecule
- E1; E2; Capsid
- UniProt
- E9KXM2, E9KXL2, P27284
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 4.4 · 4 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | E1 | protein | 430 | 7% helix, 27% strand | E9KXM2 |
| B, E, H, K | E2 | protein | 420 | 11% helix, 29% strand | E9KXL2 |
| C, I, L | Capsid | protein | 160 | 8% helix, 32% strand | P27284 |
| F | Capsid | protein | 159 | 6% helix, 31% strand | P27284 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, D, G, J, B, E, H, K
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 | 617 | 0.84 | 0.89 | 66 | empty |
| 2 | 607 | 0.84 | 0.88 | 63 | empty |
| 3 | 1171 | 0.83 | 0.84 | 109 | empty |
| 4 | 459 | 0.78 | 0.87 | 85 | empty |
| 5 | 1192 | 0.78 | 0.80 | 108 | empty |
Interfaces
26 interfaces between chains.
- G–H · 3653 Ų buried · 52 hydrogen bonds · protein-protein
- D–E · 3509 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3461 Ų buried · 40 hydrogen bonds · protein-protein
- J–K · 3440 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 747 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 56 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6MX4 · Cryoem structure of chimeric eastern equine encephalitis 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 E9KXM2
- Every structure of UniProt E9KXL2
- Every structure of UniProt P27284
- Elsewhere: RCSB PDB 6MX4 · PDBe 6MX4 · UniProt E9KXM2 · UniProt E9KXL2 · UniProt P27284
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