SMTL ID : 6b7n.1

Cryo-electron microscopy structure of porcine delta coronavirus spike protein in the pre-fusion state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 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: 6 residues within 4Å: Chain A: P.42, M.73, Y.106, T.108, H.109, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: L.55, N.57, Y.184, T.186, Q.188, Y.190 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.188 NAG-NAG.3: 3 residues within 4Å: Chain A: Q.767, G.770, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: V.480, R.494, F.495, N.509 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: P.42, M.73, Y.106, T.108, H.109, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain B: L.55, N.57, Y.184, T.186, Q.188, Y.190 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.188 NAG-NAG.8: 3 residues within 4Å: Chain B: Q.767, G.770, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: V.480, R.494, F.495, N.509 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain C: P.42, M.73, Y.106, T.108, H.109, N.224 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: L.55, N.57, Y.184, T.186, Q.188, Y.190 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.188 NAG-NAG.13: 3 residues within 4Å: Chain C: Q.767, G.770, N.771 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: V.480, R.494, F.495, N.509 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.4: 10 residues within 4Å: Chain A: Q.540, N.541, T.542, R.543, I.546, E.788, N.897, V.920, F.924 Chain B: K.625 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.9: 9 residues within 4Å: Chain B: Q.540, N.541, T.542, R.543, E.788, N.897, V.920, P.921 Chain C: K.625 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.14: 11 residues within 4Å: Chain A: K.625 Chain C: Q.540, N.541, T.542, R.543, I.546, E.788, N.897, V.920, P.921, F.924 No protein-ligand interaction detected (PLIP)

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

NAG.16: 4 residues within 4Å: Chain A: N.135, Y.136, V.137, N.167 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.145, T.147 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: T.233, N.234 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain A: Q.292, N.294, T.310, G.313, N.329 Ligand excluded by PLIP NAG.20: 6 residues within 4Å: Chain A: S.409, V.411, N.455, T.457, T.458, L.462 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.477 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.644, S.646 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: N.937, V.982, T.983, F.984, N.986 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.135, Y.136, V.137, N.167 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: N.145, T.147 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: Q.292, N.294, G.313, N.329 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain B: S.409, V.411, N.455, T.457, T.458, L.462 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.477 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.644, S.646 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain B: N.937, V.982, T.983, F.984, N.986 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.135, Y.136, V.137, N.167 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.145, T.147 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: T.233, N.234 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain C: Q.292, N.294, T.310, G.313, N.329 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain C: S.409, V.411, N.455, T.457, T.458, L.462 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.477 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.644, S.646 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain C: N.937, V.982, T.983, F.984, N.986 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shang, J. et al., Cryo-Electron Microscopy Structure of Porcine Deltacoronavirus Spike Protein in the Prefusion State. J. Virol. (2018)

Release Date

2017-10-25

Peptides

Spike protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike protein