SMTL ID : 8jn2.1 (2 other biounits)

Cryo-EM structure of dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 4 deg C (subparticle LLR-LRR)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-2-2-mer

Ligands

8 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.1: 1 residues within 4Å: Chain A: N.67 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 3 residues within 4Å: Chain C: H.149, N.153, Q.156 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain E: N.67 Chain G: P.62, R.63, D.89 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.89 NAG-NAG-BMA.6: 3 residues within 4Å: Chain E: H.149, N.153, Q.156 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 1 residues within 4Å: Chain I: N.67 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain K: H.149, N.153, Q.156 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 4 residues within 4Å: Chain M: N.67 Chain O: P.62, R.63, D.89 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:D.89 NAG-NAG-BMA.12: 3 residues within 4Å: Chain M: H.149, N.153, Q.156 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: H.149, N.153, Q.156 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: T.66, N.67, E.84 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain I: H.149, N.153, Q.156 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain K: T.66, N.67, E.84 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: ACEIKM
Membrane protein: BDFJLN
Human antibody DENV-115 heavy chain: GO
Human antibody DENV-115 light chain: HP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

I
A

K
C

M
E

B
B

D
D

F
F

J
B

L
D

N
F

G
H

O
H

H
L

P
L

Envelope protein

Membrane protein

Human antibody DENV-115 heavy chain

Human antibody DENV-115 light chain

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