SMTL ID : 8dul.1

Cryo-EM Structure of Antibody SKT05 in complex with Western Equine Encephalitis Virus spike (local refinement from VLP particles)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

1 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: 3 residues within 4Å: Chain E: W.269, T.274, N.308 No protein-ligand interaction detected (PLIP)

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

NAG.2: 3 residues within 4Å: Chain A: W.269, S.306, N.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.306, A:S.306 NAG.3: 2 residues within 4Å: Chain A: G.184, N.186 No protein-ligand interaction detected (PLIP) NAG.4: 2 residues within 4Å: Chain B: N.305, N.306 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.306 NAG.5: 2 residues within 4Å: Chain C: T.274, N.308 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.308 NAG.6: 3 residues within 4Å: Chain C: G.184, K.185, N.186 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.186 NAG.7: 2 residues within 4Å: Chain D: N.305, N.306 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain E: G.184, N.186, S.202 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.186, E:S.202, E:S.202 NAG.9: 2 residues within 4Å: Chain F: N.305, N.306 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sutton, M.S. et al., Vaccine elicitation and structural basis for antibody protection against alphaviruses. Cell (2023)

Release Date

2023-07-05

Peptides

Spike glycoprotein E2: ACE
Spike glycoprotein E1: BDF
Antibody Fab SKT05 heavy chain: G
Antibody Fab SKT05 light chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
G

E
K

B
A

D
J

F
F

G
H

H
L

Spike glycoprotein E2

Spike glycoprotein E1

Antibody Fab SKT05 heavy chain

Antibody Fab SKT05 light chain

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