SMTL ID : 7sbl.1

One RBD-up 1 of pre-fusion SARS-CoV-2 Delta variant spike protein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.44 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(Post Translational Modification)

NAG-NAG-MAN.1: 1 residues within 4Å: Chain A: 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: 3 residues within 4Å: Chain A: F.340, N.341, F.372 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 3 residues within 4Å: Chain B: F.340, N.341, F.372 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.26: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 4 residues within 4Å: Chain B: Y.487 Chain C: F.340, N.341, F.372 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.487, B:Y.487

16 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: 2 residues within 4Å: Chain A: N.614, Q.642 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.920 NAG-NAG.5: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain B: E.279, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.614, T.616 Chain C: I.832, Q.834 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 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.13: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain B: Q.115, N.163, T.165 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: N.715, L.920, Q.924 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.920 NAG-NAG.20: 4 residues within 4Å: Chain C: N.122, A.123, N.125, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain B: R.455, K.456, K.460, E.463 Chain C: T.108, N.232, T.234 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.456 NAG-NAG.22: 3 residues within 4Å: Chain B: K.556 Chain C: N.278, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain A: I.832, Q.834 Chain C: N.614, T.616 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain C: E.132, N.162, N.163 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.14: 2 residues within 4Å: Chain B: E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.25: 1 residues within 4Å: Chain C: N.1072 No protein-ligand interaction detected (PLIP)

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

NAG.30: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: N.122, N.125, V.127, M.153, E.154 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain A: N.149 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.232 Chain C: E.463 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: N.278, N.280 Chain C: K.556 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.1156 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain B: N.122, N.125, V.127, E.154 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: 2 residues within 4Å: Chain C: N.149, W.152 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

2021-11-10

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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