SMTL ID : 9dak.1

Merbecovirus PnNL2018B Spike glycoprotein RBD bound to the P. Nathusii ACE2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.1: 3 residues within 4Å: Chain A: Q.172, Q.192, N.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.197 NAG-NAG-FUC.4: 2 residues within 4Å: Chain A: N.624 Chain B: G.132 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: 4 residues within 4Å: Chain A: N.306, Y.307, S.308, H.311 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: E.243, N.367, N.370 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: H.249, R.345, N.779, S.781, D.782 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.345

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.5: 4 residues within 4Å: Chain A: H.507, D.510, S.635, N.636 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.510, A:D.510 NAG-NAG-BMA.7: 6 residues within 4Å: Chain B: N.169, H.214, A.215, G.217, N.218, T.245 No protein-ligand interaction detected (PLIP)

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

NAG.8: 2 residues within 4Å: Chain A: R.117, N.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.117, A:R.117, A:N.181 NAG.9: 1 residues within 4Å: Chain A: N.412 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain A: N.419 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain B: N.218, T.220, Y.221, T.222 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.221 Hydrogen bonds: B:T.222

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 3 residues within 4Å: Chain A: H.464, H.468, E.492 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.464, A:H.468, A:E.492

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ma, C.B. et al., Multiple independent acquisitions of ACE2 usage in MERS-related coronaviruses. Cell (2025)

Release Date

2025-02-19

Peptides

ACE2: A
Spike glycoprotein receptor binding domain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ACE2

Spike glycoprotein receptor binding domain