SMTL ID : 7sbo.1

One RBD-up 2 of pre-fusion SARS-CoV-2 Delta variant spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 4.30 Å

Oligo State

homo-trimer

Ligands

10 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.1: 2 residues within 4Å: Chain A: N.162, N.163 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.7: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 4 residues within 4Å: Chain A: F.340, N.341, L.366, F.372 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.18: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 3 residues within 4Å: Chain B: F.340, N.341, F.372 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.29: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.30: 5 residues within 4Å: Chain B: N.485, Y.487 Chain C: F.336, F.340, N.341 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.487

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.329, P.577, Q.578 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.614, T.616, Q.642 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.715, L.920, Q.1069 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.920 NAG-NAG.5: 2 residues within 4Å: Chain A: N.799, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: Q.115, E.132, N.163, T.165 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.122, N.125, V.127, S.151 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain B: E.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.614, T.616, Q.642 Chain C: I.832, Q.834 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.920 NAG-NAG.15: 2 residues within 4Å: Chain B: N.799, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain C: N.162, N.163 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain C: N.122, A.123, N.125, S.151 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain B: K.460, E.463 Chain C: T.108, N.232 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: N.278, E.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain A: I.832 Chain C: N.614, Q.642 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain C: N.715, L.920, Q.1069 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.920 NAG-NAG.26: 2 residues within 4Å: Chain C: N.799, Q.802 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: 1 residues within 4Å: Chain A: N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 1 residues within 4Å: Chain B: N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.27: 2 residues within 4Å: Chain C: E.1070, N.1072 No protein-ligand interaction detected (PLIP)

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

NAG.31: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.32: 6 residues within 4Å: Chain A: N.122, N.125, V.127, S.151, M.153, E.154 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.148, N.149 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.232 Chain C: E.463 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.278, N.280 Chain C: K.556 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain A: N.1156 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.149 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain B: N.232 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain B: N.329 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.601 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain B: N.707, G.1129 Chain C: D.794 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain B: N.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.149 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.329, Q.578 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.601 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.707, N.708 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.1156 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Membrane fusion and immune evasion by the spike protein of SARS-CoV-2 Delta variant. Science (2021)

Release Date

2021-11-03

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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