SMTL ID : 7kfb.1

Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-442

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

6 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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-MAN.1: 4 residues within 4Å: Chain A: T.221, L.258, N.261, Y.265 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.265 NAG-NAG-BMA-MAN-MAN.3: 9 residues within 4Å: Chain A: L.74, K.159, E.160, V.184 Chain D: Q.48, P.49, N.103, T.106 Chain L: F.75 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.49 NAG-NAG-BMA-MAN-MAN.4: 4 residues within 4Å: Chain E: T.221, L.258, N.261, Y.265 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.265 NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain D: F.75 Chain E: L.74, K.159, E.160, V.184 Chain H: Q.48, P.49, N.103, T.106 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:P.49 NAG-NAG-BMA-MAN-MAN.7: 4 residues within 4Å: Chain I: T.221, L.258, N.261, Y.265 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.265 NAG-NAG-BMA-MAN-MAN.9: 9 residues within 4Å: Chain H: F.75 Chain I: L.74, K.159, E.160, V.184 Chain L: Q.48, P.49, N.103, T.106 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:P.49

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.2: 2 residues within 4Å: Chain A: N.232, E.233 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain E: N.232, E.233 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain I: N.232, E.233 No protein-ligand interaction detected (PLIP)

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

NAG.10: 5 residues within 4Å: Chain A: N.272, T.273 Chain B: Y.118 Chain C: Y.50, S.54 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.118 Hydrophobic interactions: A:T.273 NAG.11: 2 residues within 4Å: Chain A: D.241, N.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.241 NAG.12: 5 residues within 4Å: Chain E: N.272, T.273 Chain F: Y.118 Chain G: Y.50, S.54 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Y.118 Hydrophobic interactions: E:T.273 NAG.13: 2 residues within 4Å: Chain E: D.241, N.242 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.241 NAG.14: 5 residues within 4Å: Chain I: N.272, T.273 Chain J: Y.118 Chain K: Y.50, S.54 2 PLIP interactions: 1 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:Y.118 Hydrophobic interactions: I:T.273 NAG.15: 2 residues within 4Å: Chain I: D.241, N.242 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.241

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

Virion spike glycoprotein 1: AEI
Antibody Fab EBOV-442 heavy chain: BFJ
Antibody Fab EBOV-442 light chain: CGK
Virion spike glycoprotein 2: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
B

I
C

B
G

F
H

J
I

C
J

G
K

K
L

D
D

H
E

L
F

Virion spike glycoprotein 1

Antibody Fab EBOV-442 heavy chain

Antibody Fab EBOV-442 light chain

Virion spike glycoprotein 2

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