SMTL ID : 7xoe.1

Cryo-EM structure of S glycoprotein encoded by the Covid-19 mRNA vaccine candidate RQ3013 (Prefusion 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(Non-covalent)(Non-functional Binders)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.120, A.121, T.122, V.125 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.122 Hydrogen bonds: A:A.121 NAG-NAG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: S.800, Q.801, N.925 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.1095, T.1097 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: I.1129, N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.1095, T.1097, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.798 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.1095, H.1098 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1098 NAG-NAG.12: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.13: 3 residues within 4Å: Chain A: E.130, N.161, N.162 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: T.106, N.231 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.613, T.615, E.616, Q.641 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: E.278, N.279 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: H.652, N.654 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.706 Chain B: D.793 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: E.1069, K.1070, N.1071 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: Y.28, T.29, N.30, N.61 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.613, T.615 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: K.555 Chain B: E.278, N.279 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.706 Chain C: D.793 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: K.1070, N.1071 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: I.831 Chain C: N.613, T.615, E.616 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 Ligands: NAG.30 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: L.919, N.922 Ligands: NAG.29 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: N.277, E.278, N.279 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: D.793 Chain C: N.706 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.1069, N.1071 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tan, S. et al., Preclinical evaluation of RQ3013, a broad-spectrum mRNA vaccine against SARS-CoV-2 variants. Sci Bull (Beijing) (2023)

Release Date

2024-02-14

Peptides

Spike glycoprotein,peptide: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein,peptide