SMTL ID : 7tey.1

Cryo-EM structure of SARS-CoV-2 Delta (B.1.617.2) spike protein

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

18 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: 3 residues within 4Å: Chain A: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) 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: 3 residues within 4Å: Chain A: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain B: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 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.9: 3 residues within 4Å: Chain B: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain B: N.1132 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: C.15, N.17, N.137 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.715, L.920, Q.924, Q.1069 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.920 NAG-NAG.15: 3 residues within 4Å: Chain C: N.799, S.801, Q.802 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: S.702, A.704, E.1070, N.1072 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.1096, T.1098, H.1099, F.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.1132 No protein-ligand interaction detected (PLIP)

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

NAG.19: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: E.132, N.162, N.163 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: T.108, N.232, T.234 Chain C: E.463 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.278, E.279, N.280 Chain C: K.556 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: N.707, G.1129 Chain B: D.794 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: N.122, A.123, T.124, N.125, V.127 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain B: E.132, N.162, N.163 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: T.108, N.232, T.234 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: K.556 Chain B: N.280 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.707, I.1128, G.1129 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.122, T.124, V.127 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: E.132, N.162, N.163 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: T.108, N.232, T.234 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.278, E.279, N.280 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: N.329, Q.578, L.580 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.341 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.707, I.1128, G.1129 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saville, J.W. et al., Structural and biochemical rationale for enhanced spike protein fitness in delta and kappa SARS-CoV-2 variants. Nat Commun (2022)

Release Date

2022-03-16

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Spike glycoprotein

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