SMTL ID : 7usa.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

21 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: 3 residues within 4Å: Chain A: A.330, G.368, N.464 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.936, L.956 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Q.1085, G.1088, N.1089, Q.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: T.836, H.837, S.838, D.839, N.1215, L.1238, Y.1242 Chain C: S.918 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.839 NAG-NAG.5: 1 residues within 4Å: Chain A: N.849 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.855, A.1241, Y.1242 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: S.694, L.696, N.740, S.742, D.743 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: A.330, G.368, N.464 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain B: N.936, L.956 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain B: Q.1085, G.1088, N.1089, Q.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 8 residues within 4Å: Chain A: S.918 Chain B: T.836, H.837, S.838, D.839, N.1215, L.1238, Y.1242 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.839 NAG-NAG.14: 1 residues within 4Å: Chain B: N.849 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: N.855, A.1241, Y.1242 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain B: S.694, L.696, N.740, S.742, D.743 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: A.330, G.368, N.464 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: N.936, L.956 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: Q.1085, G.1088, N.1089, Q.1092 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 8 residues within 4Å: Chain B: S.918 Chain C: T.836, H.837, S.838, D.839, N.1215, L.1238, Y.1242 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.839 NAG-NAG.23: 1 residues within 4Å: Chain C: N.849 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.855, A.1241, Y.1242 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain C: S.694, L.696, N.740, S.742, D.743 No protein-ligand interaction detected (PLIP)

6 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.7: 6 residues within 4Å: Chain A: L.298, N.300, R.312, W.442, H.444, Y.446 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 4 residues within 4Å: Chain A: Y.273, N.360, K.435, F.473 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.435 NAG-NAG-BMA.16: 6 residues within 4Å: Chain B: L.298, N.300, R.312, W.442, H.444, Y.446 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 4 residues within 4Å: Chain B: Y.273, N.360, K.435, F.473 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.435 NAG-NAG-BMA.25: 6 residues within 4Å: Chain C: L.298, N.300, R.312, W.442, H.444, Y.446 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 4 residues within 4Å: Chain C: Y.273, N.360, K.435, F.473 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.435

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

NAG.28: 3 residues within 4Å: Chain A: T.545, N.547, H.594 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain A: D.551, L.552, G.553, L.567, N.569, F.606 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.377, I.383 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: L.529, V.530, N.531, C.701 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: F.1307, N.1309 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain A: N.719 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.795 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.420 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.834 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: T.545, N.547, H.594 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain B: D.551, L.552, G.553, L.567, N.569, F.606 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: N.377, I.383 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain B: L.529, V.530, N.531, C.701 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: F.1307, N.1309 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.719 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.795 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.420 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.834 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: T.545, N.547, H.594 Ligand excluded by PLIP NAG.49: 6 residues within 4Å: Chain C: D.551, L.552, G.553, L.567, N.569, F.606 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.377, I.383 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain C: L.529, V.530, N.531, C.701 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: F.1307, N.1309 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.719 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.795 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.577 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain C: N.420 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.834 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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