SMTL ID : 6u7h.1

Cryo-EM structure of the HCoV-229E spike glycoprotein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: L.60, N.62, F.74, Q.75, D.115, R.197, T.198, H.200, Y.202, R.207, Y.237 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.198 NAG-NAG-BMA-MAN-MAN-MAN-MAN.6: 11 residues within 4Å: Chain B: L.60, N.62, F.74, Q.75, D.115, R.197, T.198, H.200, Y.202, R.207, Y.237 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.198 NAG-NAG-BMA-MAN-MAN-MAN-MAN.11: 11 residues within 4Å: Chain C: L.60, N.62, F.74, Q.75, D.115, R.197, T.198, H.200, Y.202, R.207, Y.237 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.198

9 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: 3 residues within 4Å: Chain A: Y.96, N.98, T.100 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Y.144, N.171, T.178, S.180 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: V.510, G.523, N.538 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: Y.96, N.98, T.100 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: Y.144, N.171, T.178, S.180 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: V.510, G.523, N.538 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: Y.96, N.98, T.100 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: Y.144, N.171, T.178, S.180 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: V.510, G.523, N.538 No protein-ligand interaction detected (PLIP)

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.4: 5 residues within 4Å: Chain A: N.243, S.245, A.250, N.251, F.269 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 5 residues within 4Å: Chain B: N.243, S.245, A.250, N.251, F.269 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain C: N.243, S.245, A.250, N.251, F.269 No protein-ligand interaction detected (PLIP)

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

NAG.16: 2 residues within 4Å: Chain A: N.147, N.148 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain A: R.129, G.130, T.131, L.133, N.220, T.222 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: Y.305, N.326, T.328 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.440 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.464 Chain B: S.720 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.518 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.542 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.663, S.665 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.671 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.714, K.717 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Q.821, N.930 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.147, N.148 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain B: R.129, G.130, T.131, L.133, N.220, T.222 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: Y.305, N.326, T.328 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.440 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.464 Chain C: S.720 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.518 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.542 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.663, S.665 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.671 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.714, K.717 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: Q.821, N.930 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.147, N.148 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain C: R.129, G.130, T.131, L.133, N.220, T.222 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: Y.305, N.326, T.328 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.440 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain A: S.720 Chain C: N.464 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.518 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.542 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.663, S.665 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.671 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.714, K.717 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: Q.821, N.930 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, Z. et al., The human coronavirus HCoV-229E S-protein structure and receptor binding. Elife (2019)

Release Date

2019-11-13

Peptides

spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

spike glycoprotein