SMTL ID : 9cb0.1

SARS-CoV-2 S protein - Accum modified

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

8 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: 1 residues within 4Å: Chain A: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.786, S.788 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.1083, H.1086, F.1088 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain B: N.702 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.786 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.1083, H.1086, F.1088 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.1086 NAG-NAG.7: 3 residues within 4Å: Chain C: N.702, L.907, Q.1056 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.786, S.788, Q.789 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.9: 2 residues within 4Å: Chain C: N.1083, H.1086 No protein-ligand interaction detected (PLIP)

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

NAG.10: 2 residues within 4Å: Chain A: F.44, N.46 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: V.105, N.106, N.107, T.109, N.110, V.112 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: T.93, N.219, T.221 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.316 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: G.324, F.327, N.328 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.694 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: E.1057, N.1059 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.1119 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.694, G.1116 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: A.691, N.1059 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: I.1117, N.1119 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: Y.13, N.46 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: T.93, N.219, T.221 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.694, G.1116 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.1059 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.1119 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caveney, N. et al., SARS-CoV-2 S protein - Accum modified. To Be Published

Release Date

2025-07-23

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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