SMTL ID : 8wzi.1

One RBD up state of Spike glycoprotein, SARS-CoV-2

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: 3 residues within 4Å: Chain A: N.282, E.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.716 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.800, S.802, Q.803 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1097, T.1099, H.1100, F.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1133 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: I.470 Chain B: N.166, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: E.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.618 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1073 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.1097, T.1099, H.1100, F.1102 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: I.1131, N.1133 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: K.560 Chain C: E.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.618 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain C: N.1073 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 1 residues within 4Å: Chain C: N.1133 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.4: 3 residues within 4Å: Chain A: S.703, A.705, N.1073 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1073

5 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.10: 2 residues within 4Å: Chain B: N.716, L.921 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 4 residues within 4Å: Chain B: N.800, S.802, Q.803, Q.934 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 4 residues within 4Å: Chain C: N.716, L.921, Q.925, Q.1070 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 3 residues within 4Å: Chain C: N.800, S.802, Q.803 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.20: 4 residues within 4Å: Chain C: N.1097, T.1099, H.1100, F.1102 No protein-ligand interaction detected (PLIP)

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

NAG.22: 2 residues within 4Å: Chain A: Y.30, N.63 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.333, P.581, Q.582 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.605, T.606 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: H.657, N.659 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.708, I.1129 Chain B: D.795 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.124, T.126, N.127 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.618, T.620, Q.646 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: Y.30, N.63 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: N.333, Q.582 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.605 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: H.657, N.659 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.708 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain B: N.124, A.125, T.126, N.127, V.129 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: R.459 Chain B: T.110, N.236, T.238 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: Y.30, N.63 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.333, Q.582, T.583 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.605 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: H.657, N.659 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain A: D.795 Chain C: N.708 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.124, T.126, N.127, V.129 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.166, N.167 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yadav, S. et al., Factors affecting macromolecule orientations in thin films formed in cryo-EM. Acta Crystallogr D Struct Biol (2024)

Release Date

2024-07-10

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein