SMTL ID : 7kex.1

Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-293

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 8 residues within 4Å: Chain C: T.220, T.221, I.222, F.238, L.258, N.261, E.262, Y.265 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.265 NAG-NAG-BMA.3: 8 residues within 4Å: Chain G: T.220, T.221, I.222, F.238, L.258, N.261, E.262, Y.265 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.265 NAG-NAG-BMA.5: 8 residues within 4Å: Chain K: T.220, T.221, I.222, F.238, L.258, N.261, E.262, Y.265 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:Y.265

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.2: 6 residues within 4Å: Chain C: L.74, R.89, E.160, G.161, A.162 Chain D: N.103 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain H Hydrogen bonds: C:R.89, H:Y.74, H:Y.74 NAG-NAG-BMA-MAN.4: 6 residues within 4Å: Chain G: L.74, R.89, E.160, G.161, A.162 Chain H: N.103 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain L Hydrogen bonds: G:R.89, L:Y.74, L:Y.74 NAG-NAG-BMA-MAN.6: 6 residues within 4Å: Chain K: L.74, R.89, E.160, G.161, A.162 Chain L: N.103 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain D Hydrogen bonds: K:R.89, D:Y.74, D:Y.74

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

NAG.7: 2 residues within 4Å: Chain C: N.232, E.233 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain C: R.223, E.239, D.241, N.242 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.239 Hydrogen bonds: C:D.241, C:N.242, C:N.242 NAG.9: 2 residues within 4Å: Chain G: N.232, E.233 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain G: R.223, E.239, D.241, N.242 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:E.239 Hydrogen bonds: G:D.241, G:N.242, G:N.242 NAG.11: 2 residues within 4Å: Chain K: N.232, E.233 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain K: R.223, E.239, D.241, N.242 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:E.239 Hydrogen bonds: K:D.241, K:N.242, K:N.242

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murin, C.D. et al., Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies. Cell Rep (2021)

Release Date

2021-04-28

Peptides

Antibody Fab EBOV-293 light chain: AEI
Antibody Fab EBOV-293 heavy chain: BFJ
Virion spike glycoprotein 1: CGK
Virion spike glycoprotein 2: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

E
K

I
L

B
G

F
H

J
I

C
A

G
B

K
C

D
D

H
E

L
F

Antibody Fab EBOV-293 light chain

Antibody Fab EBOV-293 heavy chain

Virion spike glycoprotein 1

Virion spike glycoprotein 2

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