SMTL ID : 8dww.1

Chikungunya VLP in complex with neutralizing Fab 506.A08 (asymmetric unit)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-4-4-4-4-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: R.134, G.139, N.141 No protein-ligand interaction detected (PLIP) NAG.2: 4 residues within 4Å: Chain A: K.115, T.116, K.181 Chain D: N.259 No protein-ligand interaction detected (PLIP) NAG.3: 4 residues within 4Å: Chain A: H.386 Chain D: K.276, S.339, N.341 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.276 NAG.4: 3 residues within 4Å: Chain F: R.134, G.139, N.141 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain F: K.181 Chain I: N.259 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain I: K.276, S.339, N.341, E.357 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:K.276 NAG.7: 3 residues within 4Å: Chain K: R.134, G.139, N.141 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:G.139 NAG.8: 1 residues within 4Å: Chain N: N.259 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:K.181 NAG.9: 3 residues within 4Å: Chain K: H.386 Chain N: K.276, N.341 1 PLIP interactions: 1 interactions with chain N Hydrophobic interactions: N:K.276 NAG.10: 2 residues within 4Å: Chain P: R.134, N.141 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain P: K.181 Chain S: N.259 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain S: K.276, N.341, E.357 1 PLIP interactions: 1 interactions with chain S Hydrophobic interactions: S:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Raju, S. et al., A chikungunya virus-like particle vaccine induces broadly neutralizing and protective antibodies against alphaviruses in humans. Sci Transl Med (2023)

Release Date

2023-05-31

Peptides

E1 glycoprotein: AFKP
506.A08 heavy chain: BGLQ
506.A08 light chain: CHMR
E2 glycoprotein: DINS
Capsid protein: EJOT

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

F
A

K
C

P
D

B
H

G
V

L
X

Q
Z

C
L

H
U

M
W

R
Y

D
N

I
M

N
O

S
P

E
R

J
Q

O
S

T
T

Membrane

We predict this structure to be a membrane protein.
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E1 glycoprotein

506.A08 heavy chain

506.A08 light chain

E2 glycoprotein

Capsid protein

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