SMTL ID : 7tnw.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

9 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.17, N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: E.130, N.159, N.160 Chain C: Y.348, I.465 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.613, T.615, Q.641 Chain B: Q.833 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: N.17, N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain A: Y.348, I.465 Chain B: E.130, N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: N.613, T.615, Q.641 Chain C: Q.833 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 2 residues within 4Å: Chain C: N.17, N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain B: Y.348, I.465 Chain C: E.130, N.159, N.160 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain A: Q.833 Chain C: N.613, T.615, Q.641 No protein-ligand interaction detected (PLIP)

21 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.2: 5 residues within 4Å: Chain A: N.120, T.122, N.123, K.127, F.152 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.4: 7 residues within 4Å: Chain A: T.106, N.231 Chain C: R.454, K.455, S.456, K.459, E.462 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.5: 2 residues within 4Å: Chain A: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 4 residues within 4Å: Chain A: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 3 residues within 4Å: Chain A: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 4 residues within 4Å: Chain A: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.11: 1 residues within 4Å: Chain A: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 5 residues within 4Å: Chain B: N.120, T.122, N.123, K.127, F.152 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 7 residues within 4Å: Chain A: R.454, K.455, S.456, K.459, E.462 Chain B: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 2 residues within 4Å: Chain B: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 4 residues within 4Å: Chain B: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.22: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.24: 5 residues within 4Å: Chain C: N.120, T.122, N.123, K.127, F.152 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 7 residues within 4Å: Chain B: R.454, K.455, S.456, K.459, E.462 Chain C: T.106, N.231 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 2 residues within 4Å: Chain C: E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.30: 3 residues within 4Å: Chain C: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.32: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.33: 1 residues within 4Å: Chain C: N.1131 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.9: 3 residues within 4Å: Chain A: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.20: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.31: 3 residues within 4Å: Chain C: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP)

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

NAG.34: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.340 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: Y.652, N.654 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.706 Chain B: I.791, Y.793 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.1155 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: 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: N.706 Chain C: I.791, Y.793 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.1155 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: N.328, Q.577, T.578 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.340 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: 3 residues within 4Å: Chain A: I.791, Y.793 Chain C: N.706 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: 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
C

B
A

C
B

Spike glycoprotein

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