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Cryo-EM structure of immature Zika virus

Analyse Cryo-EM structure of immature Zika virus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6LNU
Type
protein
Length
1,998 residues
Chains
6
Method
electron microscopy
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
9.0
Source
Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)
Molecule
Genome polyprotein
EC
3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
UniProt
A0A024B7W1
Pockets
3 · best druggability 0.40

Structure

electron microscopy · resolution 9.0 · 2 distinct chains · 0% helix, 0% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, CGenome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48)protein5030% helix, 0% strandA0A024B7W1
D, E, FGenome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48)protein1630% helix, 0% strandA0A024B7W1

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11160.400.7333empty
2920.360.7332empty
3560.290.7330empty

Interfaces

4 interfaces between chains.

  • B–E · 507 Ų buried · 0 hydrogen bonds · protein-protein
  • A–D · 416 Ų buried · 0 hydrogen bonds · protein-protein
  • C–F · 338 Ų buried · 0 hydrogen bonds · protein-protein
  • A–E · 38 Ų buried · 0 hydrogen bonds · protein-protein

Compared structures

  • 6LNU · Cryo-EM structure of immature zika virus · the same entry in another collection · chain A against A, TM-score 1.00

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