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
- 5Z0R
- Type
- protein
- Length
- 887 residues
- Chains
- 2
- 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
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular solute-binding protein family 1,VIRAL genome protein | protein | 442 | 47% helix, 17% strand | A0A140NCD0, A0A1D9C0W3 |
| B | Extracellular solute-binding protein family 1,VIRAL genome protein | protein | 445 | 49% helix, 18% strand | A0A140NCD0, A0A1D9C0W3 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.77 | 0.81 | 71 | GLC |
| 2 | 516 | 0.68 | 0.79 | 41 | empty |
| 3 | 320 | 0.68 | 0.82 | 27 | GLC |
| 4 | 191 | 0.58 | 0.81 | 23 | empty |
| 5 | 249 | 0.57 | 0.78 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 2678 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5Z0R · 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 5Z0R · PDBe 5Z0R · UniProt A0A140NCD0 · UniProt A0A1D9C0W3
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