SMTL ID : 6pci.1

EBOV GPdMuc (Makona) in complex with rEBOV-520 and rEBOV-548 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

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.1: 6 residues within 4Å: Chain A: L.39, K.124, E.125 Chain D: Q.48, P.49, N.103 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.49 NAG-NAG-BMA-MAN-MAN.2: 6 residues within 4Å: Chain G: L.39, K.124, E.125 Chain J: Q.48, P.49, N.103 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:P.49 NAG-NAG-BMA-MAN-MAN.3: 6 residues within 4Å: Chain M: L.39, K.124, E.125 Chain P: Q.48, P.49, N.103 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:P.49

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

NAG.4: 4 residues within 4Å: Chain A: T.186, N.226, E.227, Y.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.226, A:E.227 NAG.5: 1 residues within 4Å: Chain A: N.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.207, A:N.207 NAG.6: 2 residues within 4Å: Chain A: N.197, E.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.198 NAG.7: 3 residues within 4Å: Chain A: G.233, N.237 Chain B: Y.104 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain G: T.186, N.226, E.227, Y.230 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.226, G:E.227 NAG.9: 1 residues within 4Å: Chain G: N.207 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.207, G:N.207 NAG.10: 2 residues within 4Å: Chain G: N.197, E.198 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.198 NAG.11: 3 residues within 4Å: Chain G: G.233, N.237 Chain H: Y.104 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain M: T.186, N.226, E.227, Y.230 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:N.226, M:E.227 NAG.13: 1 residues within 4Å: Chain M: N.207 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:N.207, M:N.207 NAG.14: 2 residues within 4Å: Chain M: N.197, E.198 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:E.198 NAG.15: 3 residues within 4Å: Chain M: G.233, N.237 Chain N: Y.104 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gilchuk, P. et al., Analysis of a Therapeutic Antibody Cocktail Reveals Determinants for Cooperative and Broad Ebolavirus Neutralization. Immunity (2020)

Release Date

2020-03-11

Peptides

Virion spike glycoprotein: AGM
rEBOV-548 Fab heavy chain: BHN
rEBOV-548 Fab light chain: CIO
Virion spike glycoprotein,Virion spike glycoprotein,Ebola Virus (Makona) GP2: DJP
rEBOV-520 Fab light chain: EKQ
rEBOV-520 Fab heavy chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
B

M
C

B
H

H
I

N
J

C
K

I
L

O
M

D
D

J
E

P
F

E
Q

K
R

Q
S

F
N

L
O

R
P

Virion spike glycoprotein

rEBOV-548 Fab heavy chain

rEBOV-548 Fab light chain

Virion spike glycoprotein,Virion spike glycoprotein,Ebola Virus (Makona) GP2

rEBOV-520 Fab light chain

rEBOV-520 Fab heavy chain

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