SMTL ID : 7bub.1 (3 other biounits)

Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 6.5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-3-3-mer

Ligands

3 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 C: N.149, A.150, N.153, T.155, H.158 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.149 NAG-NAG.2: 5 residues within 4Å: Chain E: N.149, A.150, N.153, T.155 Chain G: G.102 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.149 NAG-NAG.3: 6 residues within 4Å: Chain G: N.149, A.150, N.153, T.155, H.158 Chain I: R.112 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.149

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

NAG.4: 2 residues within 4Å: Chain A: D.73 Chain C: N.67 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.67, A:D.73 NAG.5: 2 residues within 4Å: Chain E: N.67 Chain I: D.73 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain G: T.66, N.67 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:T.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, S. et al., A Human Antibody Neutralizes Different Flaviviruses by Using Different Mechanisms. Cell Rep (2020)

Release Date

2020-05-13

Peptides

SIgN-3C Fab heavy chain: AI
SIgN-3C Fab light chain: BJ
Dengue virus serotype2 E protein: CEG
Dengue virus serotype 2 M protein: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

I
H

B
I

J
L

C
B

E
A

G
C

D
E

F
D

H
F

SIgN-3C Fab heavy chain

SIgN-3C Fab light chain

Dengue virus serotype2 E protein

Dengue virus serotype 2 M protein

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