SMTL ID : 9blk.1

HCoV-OC43 Spike glycoprotein

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: 5 residues within 4Å: Chain A: F.719, D.720, N.731, T.733, A.734 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain B: F.719, D.720, N.731, T.733, A.734 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain C: F.719, D.720, N.731, T.733, A.734 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: E.925, A.926, N.929, G.933 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: E.925, A.926, N.929, G.933 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: E.925, A.926, N.929, G.933 No protein-ligand interaction detected (PLIP)

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

NAG.7: 4 residues within 4Å: Chain A: L.158, K.200, R.201, N.202 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.334, N.363, S.366, T.608 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: P.438, A.440, N.441 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.133, N.167 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: I.665, T.666, N.667 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: H.685, N.687, Y.752 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.701, Y.702, N.706 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: S.778, V.779, N.780 Chain B: T.873 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: V.1185, N.1186, T.1188, M.1190 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: V.1215, N.1216 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: L.158, K.200, R.201, N.202 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain B: N.334, N.363, S.366, T.608 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain B: P.438, A.440, N.441 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: N.133, N.167 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: I.665, T.666, N.667 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: H.685, N.687, Y.752 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: N.701, Y.702, N.706 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: S.778, V.779, N.780 Chain C: T.873 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain B: V.1185, N.1186, T.1188, M.1190 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: V.1215, N.1216 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: L.158, K.200, R.201, N.202 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.334, N.363, S.366, T.608 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: P.438, A.440, N.441 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.133, N.167 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: I.665, T.666, N.667 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: H.685, N.687, Y.752 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.701, Y.702, N.706 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: T.873 Chain C: S.778, V.779, N.780 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: V.1185, N.1186, T.1188, M.1190 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: V.1215, N.1216 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sewall, L.M. et al., Rapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy. Nat Biomed Eng (2025)

Release Date

2025-04-23

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein