SMTL ID : 6cv0.1

Cryo-electron microscopy structure of infectious bronchitis coronavirus spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

15 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: 9 residues within 4Å: Chain A: N.561, V.562 Chain B: G.749, A.750, I.751, A.754, T.755, Q.758, Q.775 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.775, B:Q.775 NAG-NAG.2: 2 residues within 4Å: Chain A: D.199, N.219 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain A: V.193, N.194, Q.198, P.701, G.703, F.704 Chain C: Y.437, Y.439 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: P.103, Q.122, L.123, F.124, N.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.122 NAG-NAG.7: 5 residues within 4Å: Chain A: I.52, H.53, N.85, T.90, S.167 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.52 NAG-NAG.8: 9 residues within 4Å: Chain B: N.561, V.562 Chain C: G.749, A.750, I.751, A.754, T.755, Q.758, Q.775 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.775, C:Q.775 NAG-NAG.9: 2 residues within 4Å: Chain B: D.199, N.219 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 8 residues within 4Å: Chain A: Y.437, Y.439 Chain B: V.193, N.194, Q.198, P.701, G.703, F.704 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: Q.122, L.123, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain B: H.53, G.55, N.85, D.88, T.90, S.167 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 9 residues within 4Å: Chain A: G.749, A.750, I.751, A.754, T.755, Q.758, Q.775 Chain C: N.561, V.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.775, A:Q.775 NAG-NAG.16: 2 residues within 4Å: Chain C: D.199, N.219 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 8 residues within 4Å: Chain B: Y.437, Y.439 Chain C: V.193, N.194, Q.198, P.701, G.703, F.704 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain C: Q.122, L.123, F.124, N.126 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain C: I.52, H.53, N.85, T.90, S.167 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.52

6 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.5: 7 residues within 4Å: Chain A: N.258, E.259, T.260, G.261, Y.333, Y.357, P.360 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.6: 7 residues within 4Å: Chain A: L.410, N.429, T.431, D.432, Y.463, G.464, Y.468 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.12: 7 residues within 4Å: Chain B: N.258, E.259, T.260, G.261, Y.333, Y.357, P.360 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.13: 7 residues within 4Å: Chain B: L.410, N.429, T.431, D.432, Y.463, G.464, Y.468 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.19: 6 residues within 4Å: Chain C: N.258, E.259, G.261, Y.333, Y.357, P.360 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.20: 7 residues within 4Å: Chain C: L.410, N.429, T.431, D.432, Y.463, G.464, Y.468 No protein-ligand interaction detected (PLIP)

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

NAG.22: 1 residues within 4Å: Chain A: N.658 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.696, T.698 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: L.649, N.651 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.573, K.784, D.925 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.565, L.567, N.929 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.160 Chain C: T.274, T.277 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: N.145, E.185 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: N.33, S.35, R.56 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain A: G.205, F.227, N.229, I.490, R.494 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: L.251, N.253, N.286 Ligands: NAG.32 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.288, S.290 Ligands: NAG.31 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.495, T.497, F.506 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: V.57, N.59 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.658 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.696, T.698 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: L.649, N.651 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.573, K.784, D.925 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.565, L.567, N.929 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: T.274, T.277 Chain B: N.160 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: N.145, E.185 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.33, S.35, R.56 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain B: G.205, F.227, N.229, I.490, R.494 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain B: L.251, N.253, N.286 Ligands: NAG.45 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain B: N.288, S.290 Ligands: NAG.44 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.495, F.506 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: V.57, N.59 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.658 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.696, T.698 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: L.649, N.651 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: N.573, K.784, D.925 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: N.565, L.567, N.929 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain B: T.277 Chain C: N.160 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: N.145, E.185 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain C: N.33, S.35, R.56, V.58 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain C: G.205, F.227, N.229, I.490, R.494 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain C: L.251, N.253, N.286 Ligands: NAG.58 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain C: N.288, S.290 Ligands: NAG.57 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain C: N.495, F.506 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain C: V.57, N.59 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shang, J. et al., Cryo-EM structure of infectious bronchitis coronavirus spike protein reveals structural and functional evolution of coronavirus spike proteins. PLoS Pathog. (2018)

Release Date

2018-04-18

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein