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Cryoem structure of venezuelan equine encephalitis virus (veev) tc-83 strain vlp in complex with Fab hveev-63
Analyse Cryoem structure of venezuelan equine encephalitis virus (veev) tc-83 strain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SFV
- Type
- protein
- Length
- 5,776 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein E1; Spike glycoprotein E2; Capsid protein; Hveev-63 Fab heavy chain…
- EC
- 3.4.21.90
- UniProt
- P05674
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Spike glycoprotein E1 | protein | 440 | 12% helix, 39% strand | P05674 |
| B, E, H, K | Spike glycoprotein E2 | protein | 418 | 14% helix, 39% strand | P05674 |
| C, F, I, L | Capsid protein (EC 3.4.21.90) | protein | 159 | 5% helix, 38% strand | P05674 |
| M, O, Q, S | Hveev-63 Fab heavy chain | protein | 218 | 1% helix, 30% strand | — |
| N, P, R, T | Hveev-63 Fab light chain | protein | 209 | 7% helix, 38% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, N, D, E, P, G, H, J, K, T
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 | 991 | 0.84 | 0.85 | 90 | empty |
| 2 | 1085 | 0.83 | 0.84 | 93 | empty |
| 3 | 1134 | 0.82 | 0.83 | 92 | empty |
| 4 | 928 | 0.75 | 0.78 | 88 | empty |
| 5 | 713 | 0.74 | 0.80 | 68 | empty |
Interfaces
36 interfaces between chains.
- A–B · 3714 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 3713 Ų buried · 34 hydrogen bonds · protein-protein
- J–K · 3638 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 3610 Ų buried · 32 hydrogen bonds · protein-protein
- S–T · 1482 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7SFV · CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in… · the same entry in another collection · chain F against F, 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 7SFV · PDBe 7SFV · UniProt P05674
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