SMTL ID : 6nzk.1

Structural basis for human coronavirus attachment to sialic acid receptors

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

NAG-NAG-BMA.1: 2 residues within 4Å: Chain A: N.143, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: R.153, I.155, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) 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.5: 2 residues within 4Å: Chain A: P.448, N.451 No protein-ligand interaction detected (PLIP) 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: 7 residues within 4Å: Chain B: R.153, I.155, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) 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.15: 2 residues within 4Å: Chain B: P.448, N.451 No protein-ligand interaction detected (PLIP) 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: 7 residues within 4Å: Chain C: R.153, I.155, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) 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.25: 2 residues within 4Å: Chain C: P.448, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 4 residues within 4Å: Chain C: V.1193, N.1194, M.1198, P.1207 No protein-ligand interaction detected (PLIP)

6 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

NAG-NAG-BMA-MAN.3: 6 residues within 4Å: Chain A: V.1223, N.1224 Chain B: N.890, D.893, Q.1014, K.1015 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.1015, B:K.1015 NAG-NAG-BMA-MAN.7: 4 residues within 4Å: Chain A: 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.13: 6 residues within 4Å: Chain B: V.1223, N.1224 Chain C: N.890, D.893, Q.1014, K.1015 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.1015, C:K.1015 NAG-NAG-BMA-MAN.17: 4 residues within 4Å: Chain B: 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.23: 6 residues within 4Å: Chain A: N.890, D.893, Q.1014, K.1015 Chain C: V.1223, N.1224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.1015, A:K.1015 NAG-NAG-BMA-MAN.27: 4 residues within 4Å: Chain C: D.728, N.739, T.741, A.742 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.742

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.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.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.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)

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

NAG.31: 3 residues within 4Å: Chain A: L.68, N.69, Q.290 No protein-ligand interaction detected (PLIP) NAG.32: 2 residues within 4Å: Chain A: N.156, L.165 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.165 NAG.33: 3 residues within 4Å: Chain A: I.674, T.675, N.676 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.674, A:N.676 NAG.34: 3 residues within 4Å: Chain A: H.694, N.696, Y.760 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.696 NAG.35: 1 residues within 4Å: Chain A: N.714 No protein-ligand interaction detected (PLIP) NAG.37: 3 residues within 4Å: Chain B: L.68, N.69, Q.290 No protein-ligand interaction detected (PLIP) NAG.38: 2 residues within 4Å: Chain B: N.156, L.165 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.165 NAG.39: 3 residues within 4Å: Chain B: I.674, T.675, N.676 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.674, B:N.676 NAG.40: 3 residues within 4Å: Chain B: H.694, N.696, Y.760 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.696 NAG.41: 1 residues within 4Å: Chain B: N.714 No protein-ligand interaction detected (PLIP) NAG.43: 3 residues within 4Å: Chain C: L.68, N.69, Q.290 No protein-ligand interaction detected (PLIP) NAG.44: 2 residues within 4Å: Chain C: N.156, L.165 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.165 NAG.45: 3 residues within 4Å: Chain C: I.674, T.675, N.676 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.674, C:N.676 NAG.46: 3 residues within 4Å: Chain C: H.694, N.696, Y.760 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.696 NAG.47: 1 residues within 4Å: Chain C: N.714 No protein-ligand interaction detected (PLIP)

3 x MJJ: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid(Non-covalent)

MJJ.36: 11 residues within 4Å: Chain A: N.37, K.39, T.41, L.90, K.91, G.92, S.93, L.95, L.96, S.97, W.100 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.90 Hydrogen bonds: A:N.37, A:K.91, A:S.93 Salt bridges: A:K.39, A:K.91 MJJ.42: 11 residues within 4Å: Chain B: N.37, K.39, T.41, L.90, K.91, G.92, S.93, L.95, L.96, S.97, W.100 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.90 Hydrogen bonds: B:N.37, B:K.91, B:S.93 Salt bridges: B:K.39, B:K.91 MJJ.48: 11 residues within 4Å: Chain C: N.37, K.39, T.41, L.90, K.91, G.92, S.93, L.95, L.96, S.97, W.100 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.90 Hydrogen bonds: C:N.37, C:K.91, C:S.93 Salt bridges: C:K.39, C:K.91

Links

RCSB   PDBe   PDBe-KB   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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