Research workbench
Structure of zika virus at a resolution of 3.1 ångström
Analyse Structure of zika virus at a resolution of 3.1 ångström in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CO8
- 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
- A0A024B7W1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | E protein | protein | 501 | 18% helix, 31% strand | A0A024B7W1 |
| B, D, F | M protein | protein | 75 | 47% helix, 0% strand | A0A024B7W1 |
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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.87 | 0.94 | 61 | empty |
| 2 | 976 | 0.79 | 0.81 | 95 | empty |
| 3 | 569 | 0.74 | 0.82 | 55 | empty |
| 4 | 582 | 0.72 | 0.80 | 53 | empty |
| 5 | 738 | 0.72 | 0.78 | 70 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1789 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1774 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1752 Ų buried · 14 hydrogen bonds · protein-protein
- C–E · 1656 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1472 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6CO8 · Structure of Zika virus at a resolution of 3.1 Angstrom · 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 A0A024B7W1
- Elsewhere: RCSB PDB 6CO8 · PDBe 6CO8 · UniProt A0A024B7W1
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