SMTL ID : 7to4.1

Structural and functional impact by SARS-CoV-2 Omicron spike mutations

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: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.328, P.576, Q.577 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.613, T.615 Chain B: I.831, Q.833 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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.5: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: C.15, N.17, N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: E.130, N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain B: N.613, T.615, Q.641 Chain C: Q.833 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 1 residues within 4Å: Chain C: N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain B: Y.348, A.349, I.465 Chain C: N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain A: I.831, Q.833 Chain C: N.613, T.615 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.6: 2 residues within 4Å: Chain A: E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 1 residues within 4Å: Chain B: N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.27: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.7: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 7 residues within 4Å: Chain B: N.120, T.122, N.123, V.125, E.149, F.152, E.164 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.12: 3 residues within 4Å: Chain A: K.555 Chain B: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.14: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.20: 8 residues within 4Å: Chain C: N.120, A.121, T.122, N.123, V.125, K.127, F.152, V.166 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.125, C:K.127 NAG-NAG-MAN.22: 7 residues within 4Å: Chain B: R.454, K.455, K.459, E.462 Chain C: T.106, N.231, T.233 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.455 Hydrophobic interactions: C:T.233 NAG-NAG-MAN.23: 2 residues within 4Å: Chain C: N.277, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.25: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.30: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.120, T.122, N.123 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.159, N.160 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: T.106, N.231 Chain C: R.454, K.455 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: N.277, E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.340 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.706 Chain B: Y.793 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.1155 Chain C: K.1154 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.231 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: D.336, N.340 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: Y.652, N.654 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: S.705, N.706 Chain C: I.791 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: Y.1152, N.1155, H.1156 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.328 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.340, T.342 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: Y.652, N.654 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain A: I.791, Y.793 Chain C: S.705, N.706 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain C: Y.1152, N.1155 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Structural and functional impact by SARS-CoV-2 Omicron spike mutations. Cell Rep (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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