SMTL ID : 7us6.1

Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprotein with domain 0 in the proximal conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

20 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: 4 residues within 4Å: Chain A: W.2, V.89, S.90, N.91 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.681, A.1067, Y.1068, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: L.124, T.125, N.126, W.268, H.270, Y.272 Ligands: BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: L.522, N.566, S.568, D.569, Y.573 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: Q.911, G.914, N.915, Q.918 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: Q.95, N.186, G.297, W.300 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: W.2, V.89, S.90, N.91 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: N.681, A.1067, Y.1068, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 7 residues within 4Å: Chain B: L.124, T.125, N.126, W.268, H.270, Y.272 Ligands: BMA-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain B: L.522, N.566, S.568, D.569, Y.573 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: Q.911, G.914, N.915, Q.918 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: W.2, V.89, S.90, N.91 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain C: N.681, A.1067, Y.1068, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain C: L.124, T.125, N.126, W.268, H.270, Y.272 Ligands: BMA-MAN-MAN.22 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain C: L.522, N.566, S.568, D.569, Y.573 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 1 residues within 4Å: Chain C: N.675 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain C: Q.911, G.914, N.915, Q.918 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: Q.95, N.186, G.297, W.300 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN: 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.2: 9 residues within 4Å: Chain A: T.662, H.663, S.664, D.665, N.1041, L.1064, Y.1068 Chain C: S.744, L.746 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.665 NAG-NAG-BMA-MAN-MAN.11: 9 residues within 4Å: Chain A: S.744, L.746 Chain B: T.662, H.663, S.664, D.665, N.1041, L.1064, Y.1068 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.665 NAG-NAG-BMA-MAN-MAN.19: 9 residues within 4Å: Chain B: S.744, L.746 Chain C: T.662, H.663, S.664, D.665, N.1041, L.1064, Y.1068 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.665

3 x BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose

BMA-MAN-MAN.5: 3 residues within 4Å: Chain A: R.138, W.268 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) BMA-MAN-MAN.14: 3 residues within 4Å: Chain B: R.138, W.268 Ligands: NAG-NAG.13 No protein-ligand interaction detected (PLIP) BMA-MAN-MAN.22: 3 residues within 4Å: Chain C: R.138, W.268 Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP)

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

NAG.27: 3 residues within 4Å: Chain A: T.371, N.373, H.420 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.11, I.14 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.84 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: A.156, V.199, N.290 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.621, Y.622, T.623 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain A: D.377, G.379, L.393, S.394, N.395, F.432 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.545 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.660 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.762, L.782 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: V.1131, F.1133, N.1135 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.403 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.246 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.203, I.209 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain A: N.357, H.523, S.526, C.527 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: T.371, N.373, H.420 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.11 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.84 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain B: A.156, V.199, N.290 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: N.621, Y.622, T.623 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain B: D.377, G.379, L.393, S.394, N.395, F.432 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.545 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain B: N.660 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain B: N.762, L.782 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain B: V.1131, F.1133, N.1135 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain B: Q.95, N.186, G.297, W.300 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain B: N.403 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain B: N.246 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain B: N.203, I.209 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain B: N.357, H.523, S.526, C.527 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: T.371, N.373, H.420 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.11 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain C: N.84 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain C: A.156, V.199, N.290 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain C: N.621, Y.622, T.623 Ligand excluded by PLIP NAG.61: 6 residues within 4Å: Chain C: D.377, G.379, L.393, S.394, N.395, F.432 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain C: N.545 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain C: N.660 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain C: N.762, L.782 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain C: V.1131, F.1133, N.1135 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain C: N.403 Ligand excluded by PLIP NAG.67: 1 residues within 4Å: Chain C: N.246 Ligand excluded by PLIP NAG.68: 2 residues within 4Å: Chain C: N.203, I.209 Ligand excluded by PLIP NAG.69: 4 residues within 4Å: Chain C: N.357, H.523, S.526, C.527 Ligand excluded by PLIP

Links

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Citation

Tortorici, M.A. et al., Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein. Cell (2022)

Release Date

2022-08-24

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein