SMTL ID : 7lww.1

Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 1-RBD-up conformation (S-GSAS-D614G-K417N-E484K-N501Y)

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(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.2: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.717, L.922, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.11: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

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

NAG.13: 4 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: S.459 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.280, E.281, N.282 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: N.331, Q.580 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.709, N.710, I.1130, G.1131 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: T.108, N.234 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain B: N.717, L.922, Q.926, Q.1071 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: F.342, N.343, V.367, S.371, F.374 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: S.708, N.709, N.710 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: N.331, P.579, Q.580, L.582 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.234 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.122, T.124, V.127, V.171 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.616, T.618 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity. Science (2021)

Release Date

2021-03-31

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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