SMTL ID : 6vkm.1

Crystal Structure of Stabilized GP from Makona Variant of Ebola Virus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 8 residues within 4Å: Chain A: E.156, A.158, V.180, Q.349, P.350, N.404, T.407 Chain B: W.372 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.350 NAG-NAG.3: 8 residues within 4Å: Chain B: E.156, A.158, V.180, Q.349, P.350, N.404, T.407 Chain C: W.372 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.350 NAG-NAG.5: 8 residues within 4Å: Chain A: W.372 Chain C: E.156, A.158, V.180, Q.349, P.350, N.404, T.407 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.350

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: T.217, L.254, N.257, Y.261 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.254 Hydrogen bonds: A:N.257 NAG.4: 4 residues within 4Å: Chain B: T.217, L.254, N.257, Y.261 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.254 Hydrogen bonds: B:N.257 NAG.6: 4 residues within 4Å: Chain C: T.217, L.254, N.257, Y.261 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.254 Hydrogen bonds: C:N.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rutten, L. et al., Structure-Based Design of Prefusion-Stabilized Filovirus Glycoprotein Trimers. Cell Rep (2020)

Release Date

2020-04-15

Peptides

Virion spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Virion spike glycoprotein