MolNFT v1 · #122512 · protein
The cryo-EM structure of zika virus
5IRE · E protein: “The cryo-EM structure of zika virus”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #122512 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IRE
- Type
- protein
- Length
- 1,728 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E protein; M protein
- UniProt
- A0A060H177, A0A096XFQ2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 2 distinct chains · 23% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | E protein | protein | 501 | 18% helix, 31% strand | A0A060H177 |
| B, D, F | M protein | protein | 75 | 60% helix, 0% strand | A0A096XFQ2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 944 | 0.82 | 0.84 | 102 | empty |
| 2 | 355 | 0.75 | 0.86 | 51 | empty |
| 3 | 547 | 0.73 | 0.81 | 55 | empty |
| 4 | 549 | 0.71 | 0.80 | 83 | empty |
| 5 | 64 | 0.70 | 0.96 | 28 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1206 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1171 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 1119 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1074 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 964 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5IRE · The cryo-EM structure of 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 A0A060H177
- Every structure of UniProt A0A096XFQ2
- Elsewhere: RCSB PDB 5IRE · PDBe 5IRE · UniProt A0A060H177 · UniProt A0A096XFQ2
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