Research workbench
Cryo-EM structure of veev vlp at the 5-fold axes
Analyse Cryo-EM structure of veev vlp at the 5-fold axes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FFO
- Type
- protein
- Length
- 1,067 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Assembly protein E3; Spike glycoprotein E2; Spike glycoprotein E1
- EC
- 3.4.21.90
- UniProt
- P05674
- Pockets
- 13 · best druggability 0.74
Structure
electron microscopy · 4 distinct chains · 14% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K | Capsid protein (EC 3.4.21.90) | protein | 163 | 10% helix, 42% strand | P05674 |
| L | Assembly protein E3 | protein | 50 | 38% helix, 12% strand | P05674 |
| N | Spike glycoprotein E2 | protein | 412 | 16% helix, 39% strand | P05674 |
| O | Spike glycoprotein E1 | protein | 442 | 12% helix, 40% strand | P05674 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.74 | 0.78 | 70 | empty |
| 2 | 374 | 0.68 | 0.81 | 39 | empty |
| 3 | 518 | 0.66 | 0.77 | 39 | empty |
| 4 | 445 | 0.62 | 0.76 | 49 | empty |
| 5 | 73 | 0.54 | 0.86 | 20 | empty |
Interfaces
4 interfaces between chains.
- N–O · 3581 Ų buried · 32 hydrogen bonds · protein-protein
- L–N · 804 Ų buried · 9 hydrogen bonds · protein-protein
- K–N · 538 Ų buried · 10 hydrogen bonds · protein-protein
- K–O · 300 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 7FFO · Cryo-EM structure of VEEV VLP at the 5-fold axes · the same entry in another collection · chain K against K, 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 P05674
- Elsewhere: RCSB PDB 7FFO · PDBe 7FFO · UniProt P05674
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