SMTL ID : 8vt2.1

cryo-EM structure of HMPV (MPV-2c)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 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: 3 residues within 4Å: Chain A: N.190, S.210 Chain B: D.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain B: N.190, S.210 Chain C: D.62, G.63, P.64 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.62 NAG-NAG-BMA.5: 3 residues within 4Å: Chain A: P.64 Chain C: N.190, S.210 No protein-ligand interaction detected (PLIP)

3 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: 2 residues within 4Å: Chain A: D.54, N.57 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.57 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain C: D.54, N.57 No protein-ligand interaction detected (PLIP)

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.7: 4 residues within 4Å: Chain A: E.367, I.370, N.371, T.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.374 NAG.8: 3 residues within 4Å: Chain B: E.367, N.371, T.374 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.374 NAG.9: 4 residues within 4Å: Chain C: E.367, I.370, N.371, T.374 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.371

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bakkers, M.J.G. et al., Efficacious human metapneumovirus vaccine based on AI-guided engineering of a closed prefusion trimer. Nat Commun (2024)

Release Date

2024-07-31

Peptides

Prefusion of HMPV (MPV-2c): ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Prefusion of HMPV (MPV-2c)