Research workbench
Cryoem structure of eastern equine encephalitis (eeev) vlp with Fab eeev-143.
Analyse Cryoem structure of eastern equine encephalitis (eeev) vlp with Fab eeev-143. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XOB
- Type
- protein
- Length
- 5,700 residues
- Chains
- 20
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Togavirin; Eeev-143 Fab heavy chain; Eeev-143 Fab light chain
- EC
- 3.4.21.90
- UniProt
- Q88678
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 9% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Togavirin (EC 3.4.21.90) | protein | 433 | 12% helix, 26% strand | Q88678 |
| B, E, H, K | Togavirin (EC 3.4.21.90) | protein | 414 | 15% helix, 24% strand | Q88678 |
| C, F, I, L | Togavirin (EC 3.4.21.90) | protein | 151 | 5% helix, 25% strand | Q88678 |
| M, O, Q, S | Eeev-143 Fab heavy chain | protein | 214 | 3% helix, 20% strand | — |
| N, P, R, T | Eeev-143 Fab light chain | protein | 213 | 0% helix, 18% strand | — |
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 | 598 | 0.82 | 0.87 | 94 | empty |
| 2 | 534 | 0.82 | 0.87 | 83 | empty |
| 3 | 455 | 0.81 | 0.89 | 72 | empty |
| 4 | 464 | 0.81 | 0.88 | 69 | empty |
| 5 | 136 | 0.81 | 0.97 | 37 | empty |
Interfaces
34 interfaces between chains.
- J–K · 2204 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2063 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1965 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1871 Ų buried · 19 hydrogen bonds · protein-protein
- Q–R · 1323 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide (disulfide).
Compared structures
- 6XOB · CryoEM structure of Eastern Equine Encephalitis (EEEV) VLP with Fab EEEV-143. · 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 Q88678
- Elsewhere: RCSB PDB 6XOB · PDBe 6XOB · UniProt Q88678
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