SMTL ID : 6mej.1

Crystal structure of Hepatitis C virus envelope glycoprotein E2 ectodomain in complex with human antibodies HEPC3 and HEPC46

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain C: D.98, N.173, T.175, F.177, K.179 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.2: 9 residues within 4Å: Chain C: N.65, S.67 Chain D: Q.3, S.25, G.26, G.27, L.29, Y.32, S.76 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.3, D:S.25, D:S.25

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

NAG.3: 3 residues within 4Å: Chain C: N.47 Chain D: Y.102 Chain E: Y.49 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: C:N.47, E:Y.49 Hydrophobic interactions: D:Y.102 NAG.4: 5 residues within 4Å: Chain A: G.26, Y.27, I.28 Chain C: C.111, N.157 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:Y.27, A:I.28 Hydrogen bonds: C:N.157 NAG.5: 3 residues within 4Å: Chain C: S.66, C.69, N.240 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.66, C:S.66, C:S.66, C:N.240 NAG.6: 3 residues within 4Å: Chain C: H.38, N.40, Y.144 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.144 Hydrogen bonds: C:N.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Flyak, A.I. et al., HCV Broadly Neutralizing Antibodies Use a CDRH3 Disulfide Motif to Recognize an E2 Glycoprotein Site that Can Be Targeted for Vaccine Design. Cell Host Microbe (2018)

Release Date

2018-11-21

Peptides

antibody HEPC46 Heavy Chain: A
antibody HEPC46 Light Chain: B
E2 glycoprotein: C
antibody HEPC3 Heavy Chain: D
antibody HEPC3 Light Chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

antibody HEPC46 Heavy Chain

antibody HEPC46 Light Chain

E2 glycoprotein

antibody HEPC3 Heavy Chain

antibody HEPC3 Light Chain

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