SMTL ID : 7tf8.1

SARS-CoV-2 Omicron 3-RBD down Spike Protein Trimer without the P986-P987 stabilizing mutations (S-GSAS-Omicron)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 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.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: T.106, N.231, T.233 Chain C: R.454, K.459, E.462 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain B: K.459, E.462 Chain C: T.106, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: S.701, A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.5: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.919 NAG-NAG-BMA-MAN.12: 2 residues within 4Å: Chain B: N.798, Q.801 No protein-ligand interaction detected (PLIP)

4 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.6: 4 residues within 4Å: Chain A: N.798, S.800, Q.801, F.814 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.9: 8 residues within 4Å: Chain A: R.454, K.455, S.456, K.459 Chain B: T.106, N.231, T.233, K.526 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.455, B:K.526, B:K.526 NAG-NAG-BMA-MAN-MAN.11: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.919 NAG-NAG-BMA-MAN-MAN.15: 5 residues within 4Å: Chain C: T.713, N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: S.701, A.703, E.1069, N.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.703 NAG-NAG-BMA.10: 4 residues within 4Å: Chain A: K.555 Chain B: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 2 residues within 4Å: Chain B: A.703, N.1071 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.703

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.8: 2 residues within 4Å: Chain B: N.61, P.628 No protein-ligand interaction detected (PLIP)

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

NAG.17: 3 residues within 4Å: Chain A: N.340, N.367, L.368 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.120 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.328, Q.577 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.613 Chain B: K.832 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.706 Chain B: I.791, Y.793 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1131 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: S.110, E.130, N.160 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.613, Q.641 Chain C: K.832 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.328, P.576, Q.577 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.706 Chain C: Y.793 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: I.1129, N.1131 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: E.278, N.279 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: Q.833 Chain C: N.613, T.615, Q.641 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: I.791, Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.1131 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: E.130, F.131, N.160, T.162 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Structural diversity of the SARS-CoV-2 Omicron spike. Mol.Cell (2022)

Release Date

2022-02-16

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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