SMTL ID : 7tf1.1

Cryo-EM structure of SARS-CoV-2 Kappa (B.1.617.1) Q484I spike protein (focused refinement of RBD)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.331, Q.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.331 NAG.2: 4 residues within 4Å: Chain A: F.338, F.342, N.343, L.368 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.342, A:L.368 NAG.3: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.331, B:P.579 NAG.4: 3 residues within 4Å: Chain B: F.338, F.342, N.343 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.342 Hydrogen bonds: B:N.343 NAG.5: 2 residues within 4Å: Chain C: N.331, Q.580 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.331 NAG.6: 4 residues within 4Å: Chain C: F.338, G.339, F.342, N.343 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.342 Hydrogen bonds: C:N.343 NAG.7: 3 residues within 4Å: Chain D: N.331, Q.580, L.582 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.331 NAG.8: 2 residues within 4Å: Chain D: F.342, N.343 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.342 Hydrogen bonds: D:N.343 NAG.9: 2 residues within 4Å: Chain E: N.331, Q.580 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.331 NAG.10: 4 residues within 4Å: Chain E: F.338, F.342, N.343, L.368 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.342, E:L.368 Hydrogen bonds: E:N.343 NAG.11: 2 residues within 4Å: Chain F: N.331, Q.580 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain F: F.342, N.343, L.368 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.342, F:L.368 Hydrogen bonds: F:N.343

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

2022-03-30

Peptides

Spike glycoprotein: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Spike glycoprotein

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