SMTL ID : 8dpm.1

Structure of EBOV GP lacking the mucin-like domain with 9.20.1A2 Fab and 6D6 scFv bound

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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-MAN.1: 21 residues within 4Å: Chain A: L.38, K.52, R.53, K.123, E.124, A.126, V.148 Chain B: Q.7, P.8, N.62, T.65 Chain C: R.98, Y.101, Y.102, D.106, Y.107, Y.187, Y.191, R.192, I.193, T.194 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:R.192, A:K.123, C:Y.187 Hydrophobic interactions: B:P.8 NAG-NAG-BMA-MAN-MAN-MAN.2: 21 residues within 4Å: Chain F: L.38, K.52, R.53, K.123, E.124, A.126, V.148 Chain G: Q.7, P.8, N.62, T.65 Chain H: R.98, Y.101, Y.102, D.106, Y.107, Y.187, Y.191, R.192, I.193, T.194 3 PLIP interactions: 1 interactions with chain H, 1 interactions with chain F, 1 interactions with chain G Hydrogen bonds: H:R.192, F:K.52, H:Y.187 Hydrophobic interactions: G:P.8 NAG-NAG-BMA-MAN-MAN-MAN.3: 21 residues within 4Å: Chain K: L.38, K.52, R.53, K.123, E.124, A.126, V.148 Chain L: Q.7, P.8, N.62, T.65 Chain M: R.98, Y.101, Y.102, D.106, Y.107, Y.187, Y.191, R.192, I.193, T.194 3 PLIP interactions: 1 interactions with chain M, 1 interactions with chain K, 1 interactions with chain L Hydrogen bonds: M:Y.187, M:R.192, K:K.123, M:Y.187 Hydrophobic interactions: L:P.8

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

NAG.4: 3 residues within 4Å: Chain A: N.196, E.197 Chain E: Y.26 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.197 Hydrogen bonds: A:N.196, A:E.197 NAG.5: 3 residues within 4Å: Chain F: N.196, E.197 Chain J: Y.26 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:E.197 Hydrogen bonds: F:N.196 NAG.6: 3 residues within 4Å: Chain K: N.196, E.197 Chain O: Y.26 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:E.197 Hydrogen bonds: K:N.196, K:E.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., The evolution and determinants of neutralization of potent head-binding antibodies against Ebola virus. Cell Rep (2023)

Release Date

2023-07-19

Peptides

Glycoprotein GP1: AFK
Glycoprotein GP2: BGL
Antibody 6D6 scFv: CHM
Antibody 9.20.1A2 Fab heavy chain: DIN
Antibody 9.20.1A2 Fab light chain: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

F
A

K
K

B
G

G
B

L
L

C
H

H
C

M
M

D
I

I
D

N
N

E
J

J
E

O
O

Glycoprotein GP1

Glycoprotein GP2

Antibody 6D6 scFv

Antibody 9.20.1A2 Fab heavy chain

Antibody 9.20.1A2 Fab light chain

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