SMTL ID : 6m15.1

Cryo-EM structures of HKU2 spike glycoproteins

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 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: F.563, T.926, N.955 Chain B: I.644 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.563 NAG-NAG.2: 3 residues within 4Å: Chain A: N.102, F.147, Q.316 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: C.149, N.152 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.303, T.305, S.306, G.310 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: L.496, N.501 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.652, N.780 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain B: F.563, T.926, N.955 Chain C: I.644 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.563 NAG-NAG.9: 3 residues within 4Å: Chain B: N.102, F.147, Q.316 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: C.149, N.152 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.303, T.305, S.306, G.310 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: L.496, N.501 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.652, N.780 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain A: I.644 Chain C: F.563, T.926, N.955 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.563 NAG-NAG.16: 3 residues within 4Å: Chain C: N.102, F.147, Q.316 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain C: C.149, N.152 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: N.303, T.305, S.306, G.310 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: L.496, N.501 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: N.652, N.780 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.7: 3 residues within 4Å: Chain A: S.957, Y.958, N.971 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.958 NAG-NAG-BMA.14: 3 residues within 4Å: Chain B: S.957, Y.958, N.971 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.958 NAG-NAG-BMA.21: 3 residues within 4Å: Chain C: S.957, Y.958, N.971 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.958

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

NAG.22: 2 residues within 4Å: Chain A: N.560, N.985 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.37, Q.224 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.118, P.156 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.273, L.449 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.356 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: E.425, N.427 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain A: S.471, S.472, F.473, F.511, N.512 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.523 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.922, N.923 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.560, N.985 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.37, Q.224 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.118, P.156 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: N.273, L.449 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.356 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: E.425, N.427 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain B: S.471, S.472, F.473, F.511, N.512 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.523 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.922, N.923 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.560, N.985 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.37, Q.224 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.118, P.156 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.273, L.449 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.356 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: E.425, N.427 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: S.471, S.472, F.473, F.511, N.512 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.523 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.922, N.923 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, J. et al., Cryo-EM structures of HKU2 and SADS-CoV spike glycoproteins provide insights into coronavirus evolution. Nat Commun (2020)

Release Date

2020-05-27

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein