SMTL ID : 8dpl.1

Structure of EBOV GP lacking the mucin-like domain with 2.1.1D5 scFv 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: 18 residues within 4Å: Chain C: Y.101, Y.102, S.104, D.106, Y.107, Y.187, Y.191, R.192, I.193, T.194 Chain J: L.38, K.52, K.123, E.124 Chain K: Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.191, C:Y.187 NAG-NAG-BMA-MAN-MAN-MAN.2: 18 residues within 4Å: Chain F: Y.101, Y.102, S.104, D.106, Y.107, Y.187, Y.191, R.192, I.193, T.194 Chain L: L.38, K.52, K.123, E.124 Chain M: Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.191, F:Y.187 NAG-NAG-BMA-MAN-MAN-MAN.3: 19 residues within 4Å: Chain I: Y.101, Y.102, S.104, D.106, Y.107, Y.187, Y.191, R.192, I.193, T.194 Chain N: L.38, K.52, K.123, E.124, V.148 Chain O: Q.7, P.8, N.62, T.65 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Y.191, I:Y.187

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

NAG.4: 3 residues within 4Å: Chain B: S.26 Chain J: N.196, E.197 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain J Hydrogen bonds: B:S.26, J:E.197, J:E.197 Hydrophobic interactions: J:E.197 NAG.5: 2 residues within 4Å: Chain L: N.196, E.197 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain E Hydrophobic interactions: L:E.197 Hydrogen bonds: L:N.196, L:E.197, L:E.197, E:S.26 NAG.6: 3 residues within 4Å: Chain H: S.26 Chain N: N.196, E.197 5 PLIP interactions: 4 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:E.197 Hydrogen bonds: N:N.196, N:E.197, N:E.197, H:S.26

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

2.1.1D5 heavy chain variable domain: ADG
2.1.1D5 light chain variable domain: BEH
6D6 single-chain variable fragment: CFI
Glycoprotein GP1: JLN
Glycoprotein GP2: KMO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

D
A

G
K

B
G

E
B

H
L

C
H

F
C

I
O

J
I

L
D

N
M

K
J

M
E

O
N

2.1.1D5 heavy chain variable domain

2.1.1D5 light chain variable domain

6D6 single-chain variable fragment

Glycoprotein GP1

Glycoprotein GP2

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