SMTL ID : 8der.1

Cryo-EM local refinement of antibody SKV16 in complex with VEEV alphavirus spike glycoprotein

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: 4 residues within 4Å: Chain E: N.212 Chain K: Y.105 Chain L: W.90, S.92 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.92 NAG-NAG.2: 4 residues within 4Å: Chain A: Y.105 Chain B: W.90, S.92 Chain G: N.212 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.92

1 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.3: 6 residues within 4Å: Chain H: N.212 Chain I: Y.105 Chain J: K.30, W.90, D.91, S.92 4 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:S.92, J:K.30, J:K.30, J:S.92 Hydrophobic interactions: I:Y.105

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

NAG.4: 3 residues within 4Å: Chain C: T.32, N.134, V.143 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.134 NAG.5: 4 residues within 4Å: Chain D: T.32, T.34, N.134, V.143 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.134 NAG.6: 4 residues within 4Å: Chain F: T.32, T.34, N.134, V.143 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:T.32

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

2023-06-28

Peptides

SKV16 Fab Heavy Chain: AIK
SKV16 Fab Light Chain: BJL
Spike glycoprotein E1: CDF
Spike glycoprotein E2: EGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

I
H

K
W

B
Y

J
L

L
V

C
G

D
E

F
F

E
C

G
B

H
A

SKV16 Fab Heavy Chain

SKV16 Fab Light Chain

Spike glycoprotein E1

Spike glycoprotein E2

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