Research workbench
Cryo-EM structure of VEEV VLP at the 2-fold axes
Analyse Cryo-EM structure of VEEV VLP at the 2-fold axes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FFQ
- Type
- protein
- Length
- 3,208 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Venezuelan equine encephalitis virus (strain TC-83)
- Molecule
- Capsid protein; Spike glycoprotein E1; assembly protein E3; Spike glycoprotein E2
- EC
- 3.4.21.90
- UniProt
- P05674
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.5 · 7 distinct chains · 14% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, S | Capsid protein (EC 3.4.21.90) | protein | 163 | 12% helix, 40% strand | P05674 |
| B, C | Spike glycoprotein E1 | protein | 442 | 11% helix, 38% strand | P05674 |
| G | Spike glycoprotein E1 | protein | 440 | 11% helix, 40% strand | P05674 |
| I, P, T | assembly protein E3 | protein | 50 | 34% helix, 12% strand | P05674 |
| J | Spike glycoprotein E2 | protein | 416 | 15% helix, 36% strand | P05674 |
| Q | Spike glycoprotein E2 | protein | 414 | 16% helix, 35% strand | P05674 |
| R | Spike glycoprotein E2 | protein | 415 | 16% helix, 39% strand | P05674 |
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 | 1200 | 0.83 | 0.84 | 96 | empty |
| 2 | 1018 | 0.76 | 0.78 | 75 | empty |
| 3 | 1032 | 0.76 | 0.78 | 76 | empty |
| 4 | 1093 | 0.74 | 0.77 | 97 | empty |
| 5 | 102 | 0.70 | 0.93 | 20 | empty |
Interfaces
20 interfaces between chains.
- B–Q · 3629 Ų buried · 36 hydrogen bonds · protein-protein
- C–R · 3623 Ų buried · 31 hydrogen bonds · protein-protein
- G–J · 3616 Ų buried · 29 hydrogen bonds · protein-protein
- J–Q · 803 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 770 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 disulfide (disulfide).
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 P05674
- Elsewhere: RCSB PDB 7FFQ · PDBe 7FFQ · UniProt P05674
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