MolNFT v1 · #141117 · protein
Structure of jev-2F2 Fab complex
5YWO · Jev E protein: “Structure of jev-2F2 Fab complex”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #141117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YWO
- Type
- protein
- Length
- 2,588 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jev E protein; Jev M protein; 2F2 light chain; 2F2 heavy chain
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 17% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Jev E protein | protein | 500 | 19% helix, 34% strand | — |
| B, D, F | Jev M protein | protein | 74 | 53% helix, 0% strand | — |
| M, Q | 2F2 light chain | protein | 215 | 6% helix, 45% strand | — |
| N, R | 2F2 heavy chain | protein | 218 | 8% helix, 51% strand | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.83 | 0.90 | 72 | empty |
| 2 | 488 | 0.77 | 0.85 | 58 | empty |
| 3 | 467 | 0.77 | 0.84 | 47 | empty |
| 4 | 573 | 0.75 | 0.82 | 74 | empty |
| 5 | 883 | 0.71 | 0.76 | 78 | empty |
Interfaces
18 interfaces between chains.
- M–N · 2183 Ų buried · 21 hydrogen bonds · protein-protein
- Q–R · 1966 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1676 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1587 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1489 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 5YWO · Structure of JEV-2F2 Fab complex · 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
- Elsewhere: RCSB PDB 5YWO · PDBe 5YWO
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