SMTL ID : 6ohw.1

Structural basis for human coronavirus attachment to sialic acid receptors. Apo-HCoV-OC43 S

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG-NAG-BMA.1: 2 residues within 4Å: Chain A: N.143, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: R.153, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 5 residues within 4Å: Chain A: V.1223, N.1224 Chain B: N.890, D.893, K.1015 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.893 NAG-NAG-BMA.4: 7 residues within 4Å: Chain A: N.344, E.348, N.373, S.376, F.380, T.617, Q.620 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.380 NAG-NAG-BMA.10: 4 residues within 4Å: Chain A: V.1193, N.1194, M.1198, P.1207 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain B: N.143, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 6 residues within 4Å: Chain B: R.153, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain B: V.1223, N.1224 Chain C: N.890, D.893, K.1015 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.893 NAG-NAG-BMA.14: 7 residues within 4Å: Chain B: N.344, E.348, N.373, S.376, F.380, T.617, Q.620 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.380 NAG-NAG-BMA.20: 4 residues within 4Å: Chain B: V.1193, N.1194, M.1198, P.1207 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain C: N.143, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 6 residues within 4Å: Chain C: R.153, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain A: N.890, D.893, K.1015 Chain C: V.1223, N.1224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.893 NAG-NAG-BMA.24: 7 residues within 4Å: Chain C: N.344, E.348, N.373, S.376, F.380, T.617, Q.620 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.380 NAG-NAG-BMA.30: 4 residues within 4Å: Chain C: V.1193, N.1194, M.1198, P.1207 No protein-ligand interaction detected (PLIP)

12 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Non-functional Binders)(Post Translational Modification)

NAG-NAG.5: 2 residues within 4Å: Chain A: P.448, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.649 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: S.786, N.788 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: E.933, A.934, N.937 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: P.448, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain B: N.649 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain B: S.786, N.788 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain B: E.933, A.934, N.937 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain C: P.448, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 1 residues within 4Å: Chain C: N.649 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain C: S.786, N.788 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: E.933, A.934, N.937 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG-NAG-BMA-MAN.7: 5 residues within 4Å: Chain A: F.727, D.728, N.739, T.741, A.742 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.742 NAG-NAG-BMA-MAN.17: 5 residues within 4Å: Chain B: F.727, D.728, N.739, T.741, A.742 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.742 NAG-NAG-BMA-MAN.27: 5 residues within 4Å: Chain C: F.727, D.728, N.739, T.741, A.742 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.742

15 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG.31: 2 residues within 4Å: Chain A: N.69, Q.290 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.156, L.165 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: I.674, T.675, N.676 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: H.694, N.696, Y.760 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.714 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.69, Q.290 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.156, L.165 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: I.674, T.675, N.676 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: H.694, N.696, Y.760 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.714 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.69, Q.290 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.156, L.165 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: I.674, T.675, N.676 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: H.694, N.696, Y.760 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.714 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Alejandra Tortorici, M. et al., Structural basis for human coronavirus attachment to sialic acid receptors. Nat.Struct.Mol.Biol. (2019)

Release Date

2019-06-05

Peptides

Spike surface glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike surface glycoprotein

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