SMTL ID : 7x7n.1

3D model of the 3-RBD up single trimeric spike protein of SARS-CoV2 in the presence of synthetic peptide SIH-5.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-6-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 Ligand excluded by PLIP NAG.2: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.3: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.4: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.1074 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: Y.28, N.61 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: N.196, G.232, I.233, N.234 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: S.112, K.113, E.132, N.165 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: G.339, F.342, N.343, S.371, F.374 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: E.654, N.657 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.801 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: D.796 Chain B: N.709 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.1074 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: Y.28, N.61 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.234 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: G.339, F.342, N.343, V.367, S.371 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.331, I.332 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: N.801, S.803 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.709, N.710 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.1074 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: Y.28, N.61 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: G.232, I.233, N.234 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.165 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: G.339, F.342, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Khatri, B. et al., A dimeric proteomimetic prevents SARS-CoV-2 infection by dimerizing the spike protein. Nat.Chem.Biol. (2022)

Release Date

2022-04-27

Peptides

Spike glycoprotein: ABC
Synthetic peptide SIH-5: DEFGHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

C
A

D
D

E
E

F
H

G
I

H
F

I
G

Spike glycoprotein

Synthetic peptide SIH-5

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