SMTL ID : 8zy5.1

Sarbecovirus RmYN02 Spike Trimer in a Locked Conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 3 residues within 4Å: Chain A: A.660, N.1028 Chain B: Q.849 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.671, Q.880 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.880 NAG-NAG.3: 3 residues within 4Å: Chain A: N.349, S.350 Chain C: S.429 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: A.660, N.1028 Chain C: Q.849 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.671, F.672, Q.880 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.880 NAG-NAG.6: 3 residues within 4Å: Chain A: S.429 Chain B: N.349, S.350 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Q.849 Chain C: A.660, N.1028 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain C: N.671, Q.880 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.880 NAG-NAG.9: 2 residues within 4Å: Chain B: S.429 Chain C: N.349 No protein-ligand interaction detected (PLIP)

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

NAG.10: 3 residues within 4Å: Chain A: N.113, G.114, Q.120 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.310, P.539, T.541, L.542 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: Q.563 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.663 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.1052, G.1053, T.1054, H.1055, F.1057 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.150 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: D.259, V.260, N.261 Chain C: R.518 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.322, S.350 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.576 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: K.24, N.26, T.61 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: S.28, L.30, N.57 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: D.102, N.103, Q.125 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: T.99, N.223 Chain C: R.431, D.441 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.617 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1088 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.113, G.114, Q.120 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: N.310, P.539, T.541, L.542 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: Q.563 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.663 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain B: N.1052, G.1053, T.1054, H.1055, F.1057 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.150 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: R.518 Chain B: D.259, V.260, N.261 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: N.322, S.350 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.576 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: K.24, N.26, T.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: S.28, L.30, N.57 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.103, Q.125 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain A: R.431, D.441, S.443, E.446 Chain B: T.99, N.223 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain B: N.617 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.1088 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.113, G.114, Q.120 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.310, P.539, L.542 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: Q.563 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.663, G.1085 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: N.1052, G.1053, T.1054, H.1055, F.1057 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.150 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain B: R.518 Chain C: D.259, V.260, N.261 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: N.322, S.350 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.576 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: K.24, N.26, T.61 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain C: S.28, L.30, N.57 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: D.102, N.103, Q.125 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain B: R.431, D.441 Chain C: T.99, N.223 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.617 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.1088 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., A locked conformation of spike protein trimer of Sarbecovirus. To Be Published

Release Date

2025-02-05

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein