SMTL ID : 8dwx.1

Chikungunya VLP in complex with neutralizing Fab 506.C01 (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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.139 NAG.2: 3 residues within 4Å: Chain B: R.134, G.139, N.141 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain C: R.134, G.139, N.141 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.139 NAG.4: 2 residues within 4Å: Chain D: R.134, N.141 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.134 NAG.5: 2 residues within 4Å: Chain A: K.181 Chain E: N.259 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain A: H.386 Chain E: K.276, S.339, N.341, E.357 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:K.276 NAG.7: 3 residues within 4Å: Chain B: K.115, T.116 Chain F: N.259 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain F: K.276, S.339, N.341 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:K.276 NAG.9: 2 residues within 4Å: Chain C: K.115 Chain G: N.259 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain C: H.386 Chain G: K.276, N.341, E.357 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:K.276 NAG.11: 3 residues within 4Å: Chain D: K.115, K.181 Chain H: N.259 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain H: K.276, N.341, E.357 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H: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: ABCD
E2 glycoprotein: EFGH
Capsid protein: IJKL
506.C01 light chain: MPRT
506.C01 heavy chain: NOQS

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
M

F
N

G
O

H
P

I
Q

J
R

K
S

L
T

M
L

P
U

R
W

T
Y

N
H

O
V

Q
X

S
Z

Membrane

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

E2 glycoprotein

Capsid protein

506.C01 light chain

506.C01 heavy chain

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