SMTL ID : 7wg7.1

Acidic Omicron Spike Trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

14 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.1: 2 residues within 4Å: Chain A: I.230, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: P.327, N.328, N.529, Q.577 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.325 NAG-NAG.3: 1 residues within 4Å: Chain A: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: A.710, E.1069, N.1071 Chain B: L.891 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1071 NAG-NAG.5: 4 residues within 4Å: Chain A: K.792, N.798, S.800, Q.801 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.800, A:S.800, A:Q.801 NAG-NAG.8: 4 residues within 4Å: Chain A: K.455, E.462 Chain B: N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain B: F.326, P.327, N.328, P.576, Q.577 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.577 NAG-NAG.10: 1 residues within 4Å: Chain B: N.714 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.798, Q.801, F.814 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.801 NAG-NAG.13: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain B: R.454, K.455, S.456 Chain C: T.106, N.231, T.233 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.328, T.330, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP)

5 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.6: 5 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100, I.1112 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.1112 NAG-NAG-BMA.7: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain B: N.1095, H.1098, F.1100 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.1100 NAG-NAG-BMA.18: 3 residues within 4Å: Chain C: N.1095, T.1097, H.1098 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.1098 NAG-NAG-BMA.19: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.20: 2 residues within 4Å: Chain A: T.122, N.123 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: D.136, M.148, S.251 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.17, P.137 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: F.339, N.340, L.368, W.433 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.613, C.614, T.615, Q.641 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain B: N.143, M.148, S.251, S.252 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: C.15, V.16, N.17, N.135 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: D.336, N.340, L.368 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.613, C.614, Q.641 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.1071 Ligands: NAG.38 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: K.1070, N.1071 Ligands: NAG.37 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.120, N.123, V.125, F.152 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain C: K.142, N.143, M.148, S.251, S.252, S.253 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain C: N.17, T.19, R.21, N.135, D.136 Ligand excluded by PLIP NAG.42: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: V.305, E.306, N.600, T.601 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: N.613, C.614, T.615, Q.641 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: N.714, Q.1068 Ligands: NAG.48 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Ligands: NAG.47 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain A: I.791, Y.793 Chain C: N.706 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Z. et al., Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell (2022)

Release Date

2022-06-22

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

C
C

Spike glycoprotein

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