SMTL ID : 7sbk.1

Closed state of pre-fusion SARS-CoV-2 Delta variant spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.10 Å

Oligo State

homo-trimer

Ligands

27 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: 6 residues within 4Å: Chain A: N.122, A.123, N.125, V.127, E.154, V.169 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.169 NAG-NAG-MAN.2: 5 residues within 4Å: Chain A: T.108, N.232, T.234 Chain C: R.455, K.460 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.3: 2 residues within 4Å: Chain A: N.278, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.5: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.6: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.10: 6 residues within 4Å: Chain A: F.336, G.337, F.340, N.341 Chain C: N.485, Y.487 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.485, C:Y.487 NAG-NAG-MAN.11: 2 residues within 4Å: Chain A: N.162, N.163 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.12: 6 residues within 4Å: Chain B: N.122, A.123, N.125, V.127, E.154, V.169 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.169 NAG-NAG-MAN.13: 5 residues within 4Å: Chain A: R.455, K.460 Chain B: T.108, N.232, T.234 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.14: 2 residues within 4Å: Chain B: N.278, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 4 residues within 4Å: Chain B: N.715, L.920, Q.924, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.17: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.19: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.20: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.21: 6 residues within 4Å: Chain A: N.485, Y.487 Chain B: F.336, G.337, F.340, N.341 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.485, A:Y.487 NAG-NAG-MAN.22: 2 residues within 4Å: Chain B: N.162, N.163 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.23: 6 residues within 4Å: Chain C: N.122, A.123, N.125, V.127, E.154, V.169 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.169 NAG-NAG-MAN.24: 5 residues within 4Å: Chain B: R.455, K.460 Chain C: T.108, N.232, T.234 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.25: 2 residues within 4Å: Chain C: N.278, N.280 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.27: 4 residues within 4Å: Chain C: N.715, L.920, Q.924, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.28: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.30: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.31: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.32: 6 residues within 4Å: Chain B: N.485, Y.487 Chain C: F.336, G.337, F.340, N.341 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.485, B:Y.487 NAG-NAG-MAN.33: 2 residues within 4Å: Chain C: N.162, N.163 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 2 residues within 4Å: Chain A: N.614 Chain B: I.832 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain B: N.614 Chain C: I.832 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain A: I.832 Chain C: N.614, T.616 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.7: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.18: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.29: 3 residues within 4Å: Chain C: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP)

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

NAG.34: 1 residues within 4Å: Chain A: N.61 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.148, N.149, W.152 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.329, Q.578 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain A: N.601 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain A: H.653, N.655 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain A: N.707, G.1129 Chain B: D.794 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain A: N.1156 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.61 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain B: N.148, N.149, W.152 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.329, Q.578 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain B: N.601 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: H.653, 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: 3 residues within 4Å: Chain C: N.148, 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: 2 residues within 4Å: Chain C: H.653, N.655 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain A: D.794 Chain C: N.707, G.1129 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
B

B
A

C
C

Spike glycoprotein

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