SMTL ID : 7n1q.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

homo-trimer

Ligands

19 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: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.328, 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, 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: N.122, T.124, V.171 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.171 NAG-NAG.10: 3 residues within 4Å: Chain B: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.613, Q.641 Chain C: Q.833 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 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.14: 3 residues within 4Å: Chain B: N.798, S.800, Q.801 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: C.15, N.17 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: N.122, T.124, N.125, E.169 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain B: Y.348, A.349 Chain C: E.132, N.164, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain B: R.454, K.455, S.456, K.459 Chain C: T.108, N.234, T.236 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.455 NAG-NAG.22: 3 residues within 4Å: Chain C: N.277, E.278, N.279 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain A: I.831, Q.833 Chain C: N.613, T.615 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain C: N.714, L.919, Q.923, Q.1068 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.919 NAG-NAG.25: 3 residues within 4Å: Chain C: 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: 3 residues within 4Å: Chain A: A.703, E.1069, 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.26: 3 residues within 4Å: Chain C: A.703, E.1069, 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.27: 4 residues within 4Å: Chain C: N.1095, T.1097, H.1098, F.1100 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 1 residues within 4Å: Chain C: N.1131 No protein-ligand interaction detected (PLIP)

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

NAG.29: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.122, T.124, N.125 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: K.147, N.148, N.149, M.153 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: N.165 Chain C: Y.348, I.465 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain A: T.108, N.234, T.236 Chain C: R.454, K.459 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: E.278, N.279 Chain C: K.555 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: G.336, F.339, N.340 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.600 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.654 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: N.706, G.1128 Chain B: D.793 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.1155 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: C.15, V.16, N.17 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: K.147, N.148, N.149 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.328 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: G.336, N.340 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.600 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: H.652, N.654 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: N.706, G.1128 Chain C: D.793 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain B: N.1155 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: K.147, N.148, N.149 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.328, Q.577 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain C: F.339, N.340, L.365 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.600 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain C: H.652, N.654 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain A: D.793 Chain C: N.706, G.1128 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain C: N.1155, H.1156 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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