MolNFT v1 · #135636 · protein
Cryo-EM structure of immature zika virus
5U4W · E protein: “Cryo-EM structure of immature zika virus”. Electron microscopy, 2 ligands (NAG, BMA), 12 pockets (best druggability 0.63). MolNFT v1 #135636 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5U4W
- Type
- protein
- Length
- 1,770 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E protein; Pr domain; Protein E; M protein
- UniProt
- A0A1B2ZC85, A0A142I5B9
- Ligands
- NAG, BMA
- Pockets
- 12 · best druggability 0.63
Structure
electron microscopy · 4 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | E protein | protein | 390 | 6% helix, 45% strand | — |
| B, D, F | Pr domain | protein | 81 | 4% helix, 56% strand | — |
| G, I, K | Protein E | protein | 66 | 71% helix, 0% strand | A0A1B2ZC85 |
| H, J, L | M protein | protein | 53 | 70% helix, 0% strand | A0A142I5B9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A, B, C, D, E, F
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains B, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.63 | 0.75 | 64 | empty |
| 2 | 366 | 0.58 | 0.76 | 45 | empty |
| 3 | 55 | 0.52 | 0.87 | 19 | empty |
| 4 | 67 | 0.52 | 0.86 | 20 | empty |
| 5 | 63 | 0.52 | 0.86 | 21 | empty |
Interfaces
15 interfaces between chains.
- A–B · 859 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 856 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 854 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 665 Ų buried · 27 hydrogen bonds · protein-protein
- C–F · 434 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5U4W · Cryo-EM Structure of Immature Zika Virus · 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 A0A1B2ZC85
- Every structure of UniProt A0A142I5B9
- Elsewhere: RCSB PDB 5U4W · PDBe 5U4W · UniProt A0A1B2ZC85 · UniProt A0A142I5B9
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