SMTL ID : 7a3o.1

Crystal structure of dengue 1 virus envelope glycoprotein in complex with the scFv fragment of the broadly neutralizing human antibody EDE1 C10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 3 residues within 4Å: Chain A: N.67 Chain E: Q.67, D.68 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:Q.67, E:Q.67, E:D.68 NAG-FUC.9: 3 residues within 4Å: Chain B: Q.67, D.68 Chain D: N.67 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.67, B:Q.67, B:D.68, B:D.68

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: P.217, Q.256, M.260, A.263 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.256 GOL.10: 4 residues within 4Å: Chain D: P.217, Q.256, M.260, A.263 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.256

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: E.126, K.128, T.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.200 Salt bridges: A:K.128 SO4.4: 2 residues within 4Å: Chain A: K.58, K.124 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.58, A:K.124 SO4.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.6: 4 residues within 4Å: Chain A: L.214, D.215, L.216, R.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.214, A:R.233 SO4.7: 3 residues within 4Å: Chain C: S.67, R.69, Q.87 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.67, C:Q.87 Salt bridges: C:R.69 SO4.8: 4 residues within 4Å: Chain B: S.63, Q.64 Chain C: R.102, T.104 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:T.104, C:T.104, B:Q.64, B:Q.64 Salt bridges: C:R.102 SO4.11: 3 residues within 4Å: Chain D: E.126, K.128, T.200 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.128 SO4.12: 2 residues within 4Å: Chain D: K.58, K.124 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.58, D:K.124 SO4.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.14: 4 residues within 4Å: Chain D: L.214, D.215, L.216, R.233 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.214, D:D.215, D:R.233 SO4.15: 3 residues within 4Å: Chain F: S.67, R.69, Q.87 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.67, F:Q.87 Salt bridges: F:R.69 SO4.16: 4 residues within 4Å: Chain E: S.63, Q.64 Chain F: R.102, T.104 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:Q.64, E:Q.64, F:T.104 Salt bridges: F:R.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, A. et al., The epitope arrangement on flavivirus particles contributes to Mab C10's extraordinary neutralization breadth across Zika and dengue viruses. Cell (2021)

Release Date

2021-12-08

Peptides

Core protein: AD
Single chain variable fragment (scFv) from antibody EDE1 C10: BE
Single chain variable fragment (scFv) from antibody EDE1 C10: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
H

E
H

C
L

F
L

Core protein

Single chain variable fragment (scFv) from antibody EDE1 C10

Single chain variable fragment (scFv) from antibody EDE1 C10

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