Research workbench
Cryoem structure of venezuelan equine encephalitis virus (veev) tc-83 strain vlp in complex with Fab hveev-63 (focus refine of the asymmetric unit)
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
- 7SFW
- Type
- protein
- Length
- 4,984 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 0.83
Structure
electron microscopy · 5 distinct chains · 10% helix, 39% 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 | 13% helix, 39% strand | P05674 |
| C, F, I, L | Capsid protein (EC 3.4.21.90) | protein | 159 | 8% helix, 38% strand | P05674 |
| M, O, Q, S | Hveev-63 Fab heavy chain | protein | 122 | 2% helix, 38% strand | — |
| N, P, R, T | Hveev-63 Fab light chain | protein | 107 | 6% helix, 46% 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 | 1078 | 0.83 | 0.84 | 96 | empty |
| 2 | 1140 | 0.82 | 0.83 | 103 | empty |
| 3 | 1105 | 0.82 | 0.83 | 89 | empty |
| 4 | 749 | 0.75 | 0.80 | 66 | empty |
| 5 | 1176 | 0.73 | 0.77 | 98 | empty |
Interfaces
36 interfaces between chains.
- G–H · 3719 Ų buried · 37 hydrogen bonds · protein-protein
- J–K · 3650 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 3647 Ų buried · 38 hydrogen bonds · protein-protein
- D–E · 3600 Ų buried · 38 hydrogen bonds · protein-protein
- O–P · 1012 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 60 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7SFW · CryoEM structure of Venezuelan Equine Encephalitis virus (VEEV) TC-83 strain VLP in… · the same entry in another collection · chain D against D, 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 7SFW · PDBe 7SFW · UniProt P05674
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