› 6hro

X-ray diffraction
2.3Å resolution

Crystal structure of Ebolavirus glycoprotein in complex with inhibitor 118a

Released:
DOI: 10.2210/pdb6hro/pdb
PDB entry 6hro coloured by chain, front view.
PDB entry 6hro coloured by chain, side view.
PDB entry 6hro coloured by chain, top view.
Source organism: Ebola virus - Mayinga, Zaire, 1976
Primary publication:
Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.
Shaikh F, Zhao Y, Alvarez L, Iliopoulou M, Lohans C, Schofield CJ, Padilla-Parra S, Siu SWI, Fry EE, Ren J, Stuart DI
OpenAccess logo J Med Chem 62 2928-2937 (2019)
PMID: 30785281

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170177 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (3 distinct):
GP1 Chain: A
Molecule details ›
Chain: A
Length: 331 amino acids
Theoretical weight: 36.39 KDa
Source organism: Ebola virus - Mayinga, Zaire, 1976
Expression system: Homo sapiens
UniProt:
  • Canonical: Q05320 (Residues: 32-312, 464-501; Coverage: 49%)
Gene name: GP
Sequence domains: Filovirus glycoprotein
GP2 Chain: B
Molecule details ›
Chain: B
Length: 168 amino acids
Theoretical weight: 18.92 KDa
Source organism: Ebola virus - Mayinga, Zaire, 1976
Expression system: Homo sapiens
UniProt:
  • Canonical: Q05320 (Residues: 502-632; Coverage: 20%)
Gene name: GP
Sequence domains: Envelope glycoprotein GP2-like, HR1-HR2

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
4 bound ligands:
Ligand NAG 5 x NAG
Ligand GOL 4 x GOL
Ligand GKZ 2 x GKZ
Ligand DMS 1 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: R32
Unit cell:
a: 115.12Å b: 115.12Å c: 308.86Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.182 0.18 0.212
Expression system: Homo sapiens

Quick links

Citations

4 review citations

Role of food nutrients and supplementation in fighting against viral infections and boosting immunity: A review.
Thirumdas et al. (2021)
3 more

3 mentions without citation

Structure-Based in Silico Screening Identifies a Potent Ebolavirus Inhibitor from a Traditional Chinese Medicine Library.
Shaikh et al. (2019)
2 more