SMTL ID : 6qd8.1

EM structure of a EBOV-GP bound to 4M0368 neutralizing antibody

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 7 residues within 4Å: Chain B: E.128 Chain D: Q.7, N.62, T.65 Chain F: T.32, N.33, S.100 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain B Hydrogen bonds: F:S.100, B:E.128 NAG-NAG-BMA.2: 7 residues within 4Å: Chain H: E.128 Chain I: Q.7, N.62, T.65 Chain K: T.32, N.33, S.100 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain H Hydrogen bonds: K:S.100, H:E.128 NAG-NAG-BMA.3: 7 residues within 4Å: Chain G: E.128 Chain J: Q.7, N.62, T.65 Chain L: T.32, N.33, S.100 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:E.128, L:S.100

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

NAG.4: 4 residues within 4Å: Chain D: N.117, K.121 Chain J: P.111, T.115 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:P.111 NAG.5: 4 residues within 4Å: Chain D: P.111, T.115 Chain I: N.117, K.121 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.111 NAG.6: 4 residues within 4Å: Chain I: P.111, T.115 Chain J: N.117, K.121 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:P.111

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diskin, R. et al., rVSV-ZEBOV induces a polyclonal and convergent B cell response with potent Ebola virus-neutralizing antibodies. Nat.Med. (N.Y.) (2019)

Release Date

2019-10-02

Peptides

Light chain: ACE
Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1: BGH
Envelope glycoprotein: DIJ
Heavy chain: FKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
Z

C
Y

E
L

B
A

G
C

H
E

D
B

I
F

J
D

F
H

K
W

L
Q

Light chain

Envelope glycoprotein,Virion spike glycoprotein,EBOV-GP1

Envelope glycoprotein

Heavy chain

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