MolNFT v1 · #141118 · protein
Jev-2H4 Fab complex
5YWP · Jev E protein: “Jev-2H4 Fab complex”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #141118 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YWP
- 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; 2H4 light chain; 2H4 heavy chain
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 16% helix, 39% 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 | 58% helix, 1% strand | — |
| M, Q | 2H4 light chain | protein | 215 | 5% helix, 49% strand | — |
| N, R | 2H4 heavy chain | protein | 218 | 6% helix, 53% strand | — |
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.85 | 0.90 | 72 | empty |
| 2 | 1050 | 0.75 | 0.77 | 121 | empty |
| 3 | 895 | 0.74 | 0.78 | 102 | empty |
| 4 | 771 | 0.70 | 0.76 | 79 | empty |
| 5 | 557 | 0.69 | 0.79 | 52 | empty |
Interfaces
19 interfaces between chains.
- M–N · 1948 Ų buried · 33 hydrogen bonds · protein-protein
- Q–R · 1928 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1564 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1501 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1461 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 disulfide (disulfide).
Compared structures
- 5YWP · JEV-2H4 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 5YWP · PDBe 5YWP
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