SMTL ID : 8y3j.2 (3 other biounits)

Cryo-EM structure of dengue virus serotype 2 strain D2Y98P-PP1 at 4 deg C

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-15-15-mer

Ligands

15 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: 5 residues within 4Å: Chain A: N.149, N.153, T.155, K.157, H.158 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.157 NAG-NAG.2: 7 residues within 4Å: Chain C: N.149, N.153, T.155, G.156, K.157, H.158 Chain E: G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain C: G.102 Chain E: N.149, N.153, T.155, G.156, K.157, H.158 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain G: N.149, N.153, T.155, K.157, H.158 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:K.157 NAG-NAG.8: 7 residues within 4Å: Chain I: N.149, N.153, T.155, G.156, K.157, H.158 Chain K: G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain I: G.102 Chain K: N.149, N.153, T.155, G.156, K.157, H.158 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain M: N.149, N.153, T.155, K.157, H.158 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:K.157 NAG-NAG.14: 7 residues within 4Å: Chain O: N.149, N.153, T.155, G.156, K.157, H.158 Chain Q: G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain O: G.102 Chain Q: N.149, N.153, T.155, G.156, K.157, H.158 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain S: N.149, N.153, T.155, K.157, H.158 1 PLIP interactions: 1 interactions with chain S Hydrophobic interactions: S:K.157 NAG-NAG.20: 7 residues within 4Å: Chain U: N.149, N.153, T.155, G.156, K.157, H.158 Chain W: G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain U: G.102 Chain W: N.149, N.153, T.155, G.156, K.157, H.158 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain Y: N.149, N.153, T.155, K.157, H.158 1 PLIP interactions: 1 interactions with chain Y Hydrophobic interactions: Y:K.157 NAG-NAG.26: 7 residues within 4Å: Chain 0: N.149, N.153, T.155, G.156, K.157, H.158 Chain 2: G.102 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 7 residues within 4Å: Chain 0: G.102 Chain 2: N.149, N.153, T.155, G.156, K.157, H.158 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: N.67, M.118 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain C: N.67, R.89, F.90, M.118 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain E: N.67, R.89, F.90 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain G: N.67, M.118 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain I: N.67, R.89, F.90, M.118 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain K: N.67, R.89, F.90 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain M: N.67, M.118 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain O: N.67, R.89, F.90, M.118 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain Q: N.67, R.89, F.90 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain S: N.67, M.118 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain U: N.67, R.89, F.90, M.118 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain W: N.67, R.89, F.90 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain Y: N.67, M.118 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain 0: N.67, R.89, F.90, M.118 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain 2: N.67, R.89, F.90 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fibriansah, G. et al., Role of N-glycosylation at asparagine 153 of dengue envelope protein in immune response. To Be Published

Release Date

2025-01-29

Peptides

Envelope protein: ACEGIKMOQSUWY02
Membrane polyprotein: BDFHJLNPRTVXZ13

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
A

I
C

K
E

M
A

O
C

Q
E

S
A

U
C

W
E

Y
A

0
C

2
E

B
B

D
D

F
F

H
B

J
D

L
F

N
B

P
D

R
F

T
B

V
D

X
F

Z
B

1
D

3
F

Envelope protein

Membrane polyprotein

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