SMTL ID : 9iz9.1

VLP structure of Chikungunya virus complexed with C37 Fab, 2f block.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.1: 4 residues within 4Å: Chain C: R.134, G.139, N.141, R.340 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.340 NAG-NAG-BMA-FUC.2: 3 residues within 4Å: Chain D: R.134, G.139, N.141 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.4: 3 residues within 4Å: Chain F: R.134, G.139, N.141 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:R.340

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.3: 8 residues within 4Å: Chain E: E.32, L.34, R.134, L.136, G.139, N.141, D.311, R.340 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-NAG.5: 7 residues within 4Å: Chain C: L.42, K.115, T.116, F.118, P.208, E.209 Chain G: N.259 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.209 NAG-NAG-BMA-MAN-NAG.9: 9 residues within 4Å: Chain E: L.42, S.43, L.44, K.115, T.116, F.118, T.207, E.209 Chain I: N.259 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:E.209, E:L.44 NAG-NAG-BMA-MAN-NAG.11: 6 residues within 4Å: Chain F: L.44, K.115, T.116, F.118, E.209 Chain J: N.259 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.209, F:L.44, F:L.44

3 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.6: 3 residues within 4Å: Chain G: K.276, N.341, E.357 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 4 residues within 4Å: Chain H: K.276, S.339, N.341, E.357 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain E: H.386 Chain I: N.341, E.357 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.7: 6 residues within 4Å: Chain D: K.115, T.116, F.118, T.207, N.264 Chain H: N.259 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:N.264 Hydrogen bonds: D:Y.122, D:T.207

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.12: 3 residues within 4Å: Chain J: K.276, N.341, E.357 No protein-ligand interaction detected (PLIP)

4 x CLR: CHOLESTEROL(Covalent)

CLR.13: 13 residues within 4Å: Chain D: L.397, G.398, V.399, Q.400, I.402, V.410 Chain H: I.351, I.352, Y.355, Y.359, M.362, T.363, V.366 9 PLIP interactions: 7 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:I.351, H:I.352, H:Y.355, H:Y.359, H:Y.359, H:M.362, H:V.366, D:L.397, D:I.402 CLR.14: 12 residues within 4Å: Chain F: L.397, G.398, V.399, I.402, A.406 Chain J: I.351, Y.355, Y.359, M.362, T.363, V.366, V.367 11 PLIP interactions: 3 interactions with chain F, 8 interactions with chain J Hydrophobic interactions: F:V.399, F:I.402, F:A.406, J:I.351, J:Y.355, J:Y.355, J:Y.355, J:Y.359, J:Y.359, J:Y.359, J:V.367 CLR.15: 10 residues within 4Å: Chain C: L.397, S.403 Chain G: I.351, I.352, Y.355, Y.359, T.361, M.362, T.363, V.366 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:I.351, G:I.352, G:Y.355, G:Y.355, G:Y.355, G:Y.359, G:Y.359, G:Y.359, G:Y.359, G:M.362, G:V.366, C:L.397 CLR.16: 10 residues within 4Å: Chain E: G.398, V.399, Q.400, S.403 Chain I: I.352, Y.355, Y.359, M.362, T.363, V.366 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:I.352, I:Y.355, I:Y.355, I:Y.359, I:Y.359, I:Y.359, I:M.362, I:T.363, I:V.366, I:V.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, X. et al., VLP structure of Chikungunya virus complexed with C37 Fab, 2f block. To Be Published

Release Date

2025-08-06

Peptides

C37 Fab, Heavy chain: AOQS
C37 Fab, Light chain: BPRT
CHIKV E1: CDEF
Structural polyprotein: GHIJ
CHIKV capsid protein: KLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

O
Q

Q
O

S
M

B
T

P
R

R
P

T
N

C
A

D
B

E
C

F
D

G
E

H
F

I
G

J
H

K
I

L
J

M
K

N
L

Membrane

We predict this structure to be a membrane protein.
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C37 Fab, Heavy chain

C37 Fab, Light chain

CHIKV E1

Structural polyprotein

CHIKV capsid protein

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