SMTL ID : 6mei.1

Crystal structure of broadly neutralizing antibody HEPC3 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 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: 9 residues within 4Å: Chain A: N.65, S.67 Chain B: S.25, G.26, G.27, L.29, N.30, Y.32, S.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.25, B:S.25

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: 8 residues within 4Å: Chain A: N.47, S.49 Chain B: Y.102 Chain C: Y.49, N.53, S.56, G.57, S.60 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.57, C:S.60 NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: N.173, S.174, T.175, F.177, K.179 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: H.38, N.40, Y.144 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.40 NAG.5: 2 residues within 4Å: Chain A: N.149, T.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.149 Water bridges: A:T.151 NAG.6: 4 residues within 4Å: Chain A: G.112, T.113, N.157 Ligands: BR.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.113, A:N.157 NAG.7: 4 residues within 4Å: Chain A: P.70, N.240, N.262, G.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.262, A:G.264, A:G.264 Water bridges: A:N.262 NAG.8: 3 residues within 4Å: Chain A: N.34 Chain B: R.107 Chain C: N.30 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:N.30, B:R.107 Water bridges: A:N.34

7 x BR: BROMIDE ION(Non-covalent)(Non-functional Binders)

BR.9: 5 residues within 4Å: Chain A: R.72, Y.102, Y.235, P.236, C.237 Ligand excluded by PLIP BR.10: 1 residues within 4Å: Ligands: NAG.6 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain A: Y.60, T.61, H.62 Ligand excluded by PLIP BR.12: 4 residues within 4Å: Chain A: H.51 Chain B: Q.1, V.2, R.101 Ligand excluded by PLIP BR.13: 3 residues within 4Å: Chain B: W.47 Chain C: T.97, F.98 Ligand excluded by PLIP BR.14: 4 residues within 4Å: Chain A: A.56 Chain B: E.33, R.97, G.99 Ligand excluded by PLIP BR.15: 4 residues within 4Å: Chain C: I.2, Q.3, G.26, Q.27 Ligand excluded by PLIP

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

E2 glycoprotein: A
antibody HEPC3 Heavy Chain: B
antibody HEPC3 Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

E2 glycoprotein

antibody HEPC3 Heavy Chain

antibody HEPC3 Light Chain

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