Research workbench
Structural insight into the zika virus capsid encapsulating the viral genome
Analyse Structural insight into the zika virus capsid encapsulating the viral genome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z0V
- Type
- protein
- Length
- 1,769 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular solute-binding protein family 1,VIRAL genome protein
- UniProt
- A0A140NCD0, A0A1D9C0W3
- Ligands
- GLC
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Extracellular solute-binding protein family 1,VIRAL genome protein | protein | 444 | 50% helix, 18% strand | A0A140NCD0, A0A1D9C0W3 |
| B | Extracellular solute-binding protein family 1,VIRAL genome protein | protein | 441 | 50% helix, 17% strand | A0A140NCD0, A0A1D9C0W3 |
| D | Extracellular solute-binding protein family 1,VIRAL genome protein | protein | 440 | 49% helix, 18% strand | A0A140NCD0, A0A1D9C0W3 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.83 | 0.83 | 118 | empty |
| 2 | 918 | 0.79 | 0.81 | 79 | GLC |
| 3 | 641 | 0.77 | 0.82 | 50 | empty |
| 4 | 870 | 0.77 | 0.80 | 77 | empty |
| 5 | 754 | 0.76 | 0.80 | 62 | empty |
Interfaces
5 interfaces between chains.
- A–D · 2698 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 2670 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 432 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 374 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Z0V · Structural insight into the Zika virus capsid encapsulating the viral genome · 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 A0A140NCD0
- Every structure of UniProt A0A1D9C0W3
- Elsewhere: RCSB PDB 5Z0V · PDBe 5Z0V · UniProt A0A140NCD0 · UniProt A0A1D9C0W3
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