› 5kvd

X-ray diffraction
1.65Å resolution

Zika specific antibody, ZV-2, bound to ZIKA envelope DIII

Released:
DOI: 10.2210/pdb5kvd/pdb
PDB entry 5kvd coloured by chain, front view.
PDB entry 5kvd coloured by chain, side view.
PDB entry 5kvd coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis of Zika Virus-Specific Antibody Protection.
Zhao H, Fernandez E, Dowd KA, Speer SD, Platt DJ, Gorman MJ, Govero J, Nelson CA, Pierson TC, Diamond MS, Fremont DH
Cell 166 1016-1027 (2016)
PMID: 27475895

Function and Biology Details

Reactions catalysed: 
Selective hydrolysis of -Xaa-Xaa-|-Yaa- bonds in which each of the Xaa can be either Arg or Lys and Yaa can be either Ser or Ala.
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-207337 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Zika Envelope DIII Chain: E
Molecule details ›
Chain: E
Length: 110 amino acids
Theoretical weight: 11.94 KDa
Source organism: Zika virus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A0X8GJ44 (Residues: 588-697; Coverage: 3%)
Sequence domains: Flavivirus glycoprotein, immunoglobulin-like domain
Structure domains: Immunoglobulin-like
ZV-2 Antibody Fab Light Chain Chain: L
Molecule details ›
Chain: L
Length: 220 amino acids
Theoretical weight: 24.08 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins
ZV-2 Antibody Fab Heavy Chain Chain: H
Molecule details ›
Chain: H
Length: 222 amino acids
Theoretical weight: 24.02 KDa
Source organism: Mus musculus
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand NA 2 x NA
Ligand MES 1 x MES
Ligand EDO 1 x EDO
1 modified residue:
Ligand PCA 1 x PCA

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 39.02Å b: 113.44Å c: 132.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.19 0.221
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

50 review citations

Zika Virus: Immunity and Vaccine Development.
Pierson et al. (2016)
49 more

11 mentions without citation

The A-Z of Zika drug discovery.
Mottin et al. (2018)
10 more