SMTL ID : 8dun.1

Cryo-EM Structure of Antibody SKW11 in complex with Western Equine Encephalitis Virus spike (local refinement from VLP particles)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

2 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 D: N.186, S.202 Chain L: D.1 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: Q.3 Chain F: G.184, N.186 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain C: E.301, M.302, N.305 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.305 NAG.4: 2 residues within 4Å: Chain D: W.269, N.308 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.308 NAG.5: 4 residues within 4Å: Chain E: E.301, M.302, N.305 Chain F: K.119 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain F: S.306, N.308 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.308 NAG.7: 3 residues within 4Å: Chain G: E.301, M.302, N.305 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain H: N.186 Chain J: I.2 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.186 NAG.9: 2 residues within 4Å: Chain H: S.306, N.308 No protein-ligand interaction detected (PLIP)

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

Antibody SKW11 heavy chain: AIK
Antibody SKW11 light chain: BJL
Spike glycoprotein E1: CEG
Spike glycoprotein E2: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

I
I

K
N

B
L

J
M

L
O

C
A

E
F

G
J

D
B

F
G

H
K

Antibody SKW11 heavy chain

Antibody SKW11 light chain

Spike glycoprotein E1

Spike glycoprotein E2

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