SMTL ID : 7toy.1

Delta (B.1.617.2) SARS-CoV-2 variant spike protein (S-GSAS-Delta) in the 3-RBD-down conformation; Subclassification D6 state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG-NAG.1: 8 residues within 4Å: Chain A: N.232 Chain C: R.455, K.456, S.457, N.458, L.459, E.463, D.465 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.456, C:E.463 NAG-NAG.2: 4 residues within 4Å: Chain A: N.715, L.920, Q.924, Q.1069 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain A: R.455, K.456, S.457, N.458, E.463 Chain B: T.108, N.232, T.234 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.456 NAG-NAG.7: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: I.1130, N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 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.10: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 8 residues within 4Å: Chain B: R.455, S.457, N.458, E.463, Y.471 Chain C: T.108, N.232, T.234 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.455, B:S.457, B:S.457 NAG-NAG.12: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP)

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

NAG.15: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.16: 5 residues within 4Å: Chain A: N.122, T.124, N.125, V.127, V.169 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.280 Chain C: K.556 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.329, Q.578 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: F.336, G.337, N.341, L.366 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.601, T.602 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.614, T.616 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.655 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.707, G.1129 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.1072 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: T.114, Q.115, E.132, F.133, N.163 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.329, Q.578 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain B: G.337, F.340, N.341, L.366 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: N.601, T.602 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain B: Y.28, N.30, N.61 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.655 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.122, N.125 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: K.556 Chain B: N.278, E.279, N.280 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: E.132, N.163 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.614, T.616, E.617 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.707 Chain C: I.792, D.794 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.1072 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: Y.28, F.59, N.61 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain B: K.556 Chain C: N.280 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.329, Q.578 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.601, T.602 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.1072 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: G.337, N.341 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.614, T.616 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: E.132, N.163, C.164, T.165 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain C: N.655 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: D.794 Chain C: N.707, G.1129 Ligand excluded by PLIP NAG.47: 5 residues within 4Å: Chain C: N.122, T.124, N.125, V.127, V.169 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gobeil, S.M. et al., Structural diversity of the SARS-CoV-2 Omicron spike. Mol.Cell (2022)

Release Date

2022-02-09

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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