SMTL ID : 8jn5.3 (2 other biounits)

Cryo-EM structure of dengue virus serotype 3 strain 863DK in complex with human antibody DENV-290 Fab at 37 deg C (subparticle LLR-LRR)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

2 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(1-3)-[beta-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-BMA.1: 2 residues within 4Å: Chain A: N.67, Y.90 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-BMA.3: 12 residues within 4Å: Chain C: N.67, Y.90 Chain G: Y.59, Y.60, D.62, K.65, P.106, W.107 Chain H: W.31, L.98, H.99, L.100 5 PLIP interactions: 1 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:D.62, G:Y.59, H:H.99, H:L.100 Hydrophobic interactions: H:W.31, H:L.98

2 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.2: 4 residues within 4Å: Chain A: H.149, N.153, T.155, Q.156 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain E: H.149, N.153, Q.156 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 4 residues within 4Å: Chain C: H.149, N.153, T.155, Q.156 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain E: T.66, N.67 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fibriansah, G. et al., Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants. To Be Published

Release Date

2024-06-12

Peptides

Envelope protein: ACE
Membrane protein: BDF
Human antibody DENV-290 heavy chain: G
Human antibody DENV-290 light chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
L

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Envelope protein

Membrane protein

Human antibody DENV-290 heavy chain

Human antibody DENV-290 light chain

Related Entries With Identical Sequence