Research workbench
Models of E1, E2 and cp of venezuelan equine encephalitis virus tc-83 strain restrained by a near atomic resolution cryo-EM MAP
Analyse Models of E1, E2 and cp of venezuelan equine encephalitis virus 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
- 3J0C
- Type
- protein
- Length
- 4,108 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E1 envelope glycoprotein; E2 envelope glycoprotein; Capsid protein
- EC
- 3.4.21.90
- UniProt
- P05674
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 13% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | E1 envelope glycoprotein | protein | 442 | 13% helix, 42% strand | P05674 |
| B, E, H, K | E2 envelope glycoprotein | protein | 423 | 14% helix, 39% strand | P05674 |
| C, F, I, L | Capsid protein (EC 3.4.21.90) | protein | 162 | 13% helix, 46% 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 | 1008 | 0.86 | 0.87 | 115 | empty |
| 2 | 1085 | 0.84 | 0.85 | 107 | empty |
| 3 | 1156 | 0.84 | 0.85 | 103 | empty |
| 4 | 872 | 0.79 | 0.81 | 82 | empty |
| 5 | 1099 | 0.78 | 0.80 | 99 | empty |
Interfaces
26 interfaces between chains.
- D–E · 3384 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 3356 Ų buried · 36 hydrogen bonds · protein-protein
- J–K · 3215 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 3135 Ų buried · 35 hydrogen bonds · protein-protein
- E–H · 730 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 44 disulfide (disulfide).
Compared structures
- 3J0C · Models of E1, E2 and CP of Venezuelan Equine Encephalitis Virus TC-83 strain restrained… · 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 P05674
- Elsewhere: RCSB PDB 3J0C · PDBe 3J0C · UniProt P05674
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