SMTL ID : 7n1y.1

Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

16 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: N.17, N.135 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: 3 residues within 4Å: Chain A: N.613, T.615, Q.641 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.714, L.919, N.922, Q.1068 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.919 Hydrogen bonds: A:N.922 NAG-NAG.5: 2 residues within 4Å: Chain A: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain B: C.15, N.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.135 NAG-NAG.10: 5 residues within 4Å: Chain B: N.120, T.122, N.123, E.151, F.154 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain A: K.555 Chain B: N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.613, T.615, Q.641 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain B: N.714, L.919, Q.1068 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain B: N.798, S.800 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain C: N.328, P.576 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 1 residues within 4Å: Chain C: N.613 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: N.714, L.919, N.922 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain C: K.792, N.798, S.800, Q.801 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: 4 residues within 4Å: Chain A: A.703, E.1069, K.1070, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.15: 3 residues within 4Å: Chain B: A.703, E.1069, N.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.23: 2 residues within 4Å: Chain C: A.703, N.1071 No protein-ligand interaction detected (PLIP)

6 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.16: 4 residues within 4Å: Chain B: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 1 residues within 4Å: Chain B: N.1131 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.24: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.25: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.26: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: N.120, T.122, N.123, F.154 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain A: K.144, N.146 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: E.130, N.162 Chain C: Y.393 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain A: N.231 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.340, V.364 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.600, T.601 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain A: N.706 Chain B: D.793 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.1155 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: K.144, N.146 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: Y.393 Chain B: N.162 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: G.229, I.230, N.231 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: N.328, T.330, Q.577 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: G.336, N.340, S.368 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.654 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.706, G.1128 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain B: N.1155, P.1159 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.61 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.120, T.122, N.123 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain C: K.144, N.146, S.148 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.162 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain B: E.462 Chain C: N.231 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.279 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: N.340, V.364, L.365 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain C: N.654 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain A: I.791, D.793 Chain C: S.705, N.706, G.1128 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain C: N.1155 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cai, Y. et al., Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants. Science (2021)

Release Date

2021-07-07

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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