SMTL ID : 6dzm.1

Bundibugyo virus GP (mucin-deleted) in complex with pan-ebolavirus human antibody ADI-15878 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

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: 5 residues within 4Å: Chain A: Q.203, V.204, N.225, E.226, Y.229 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.229 Hydrogen bonds: A:Y.229 NAG-NAG.3: 5 residues within 4Å: Chain E: Q.203, V.204, N.225, E.226, Y.229 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.229 Hydrogen bonds: E:Y.229 NAG-NAG.5: 5 residues within 4Å: Chain I: Q.203, V.204, N.225, E.226, Y.229 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.229 Hydrogen bonds: I:Y.229

3 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.2: 7 residues within 4Å: Chain A: L.38, E.124, V.148 Chain B: N.62 Chain C: D.50 Chain D: R.100, V.101 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.100, D:R.100, C:D.50, C:D.50 NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain E: L.38, E.124, V.148 Chain F: N.62 Chain G: D.50 Chain H: R.100, V.101 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G Hydrogen bonds: H:R.100, H:R.100, G:D.50, G:D.50 NAG-NAG-BMA-MAN-MAN.6: 7 residues within 4Å: Chain I: L.38, E.124, V.148 Chain J: N.62 Chain K: D.50 Chain L: R.100, V.101 4 PLIP interactions: 2 interactions with chain L, 2 interactions with chain K Hydrogen bonds: L:R.100, L:R.100, K:D.50, K:D.50

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

NAG.7: 1 residues within 4Å: Chain A: N.196 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain B: N.117 Chain J: L.103 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:L.103 NAG.9: 1 residues within 4Å: Chain E: N.196 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain B: L.103 Chain F: N.117 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.103 NAG.11: 1 residues within 4Å: Chain I: N.196 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain F: L.103 Chain J: N.117 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:L.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murin, C.D. et al., Structural Basis of Pan-Ebolavirus Neutralization by an Antibody Targeting the Glycoprotein Fusion Loop. Cell Rep (2018)

Release Date

2018-09-12

Peptides

Bundibugyo virus GP1: AEI
Bundibugyo virus GP2: BFJ
Antibody ADI-15878 Fab, light chain: CGK
Antibody ADI-15878 Fab, heavy chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
B

I
C

B
D

F
E

J
F

C
H

G
K

K
L

D
G

H
I

L
J

Bundibugyo virus GP1

Bundibugyo virus GP2

Antibody ADI-15878 Fab, light chain

Antibody ADI-15878 Fab, heavy chain

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