SMTL ID : 6xkl.1

SARS-CoV-2 HexaPro S One RBD up

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

11 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: 2 residues within 4Å: Chain A: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: F.342, N.343, F.374 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: A.706, E.1072, N.1074 Chain B: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: A.706, N.1074 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 1 residues within 4Å: Chain C: N.801 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 No protein-ligand interaction detected (PLIP)

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

NAG.12: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.122, V.127 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain B: E.132, N.165 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: N.280, N.282 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain B: F.342, N.343, F.374 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: N.709, G.1131 Chain C: D.796 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.717, Q.1071 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.1098, H.1101 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: F.342, N.343 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hsieh, C.L. et al., Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science (2020)

Release Date

2020-07-15

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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