SMTL ID : 7y42.1

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein in complex with all-trans retinoic acid

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: Y.2, N.35 Ligand excluded by PLIP NAG.2: 2 residues within 4Å: Chain A: N.96, N.99 Ligand excluded by PLIP NAG.3: 4 residues within 4Å: Chain A: N.254, E.255, N.256 Chain C: K.532 Ligand excluded by PLIP NAG.4: 3 residues within 4Å: Chain A: N.305, Q.554, L.556 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: G.313, N.317, S.345 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.577 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.631 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.683 Chain B: D.770 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: Y.2, N.35 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: N.96, N.99 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: K.532 Chain B: N.254, E.255, N.256 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.305, Q.554, L.556 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: G.313, N.317, S.345 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.577 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.590 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.631 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.683 Chain C: D.770 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain C: Y.2, N.35 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain C: N.96, N.99 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: K.532 Chain C: N.254, E.255, N.256 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.305, Q.554, L.556 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: G.313, N.317, S.345 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.577 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.631 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: D.770 Chain C: N.683 Ligand excluded by PLIP

3 x REA: RETINOIC ACID(Non-covalent)

REA.10: 12 residues within 4Å: Chain A: F.316, A.337, Y.339, L.342, Y.343, F.348, F.351, C.406, I.408, L.487 Chain C: R.382, Q.383 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.316, A:A.337, A:Y.339, A:Y.339, A:L.342, A:Y.343, A:F.348, A:F.351, A:F.351, A:I.408, A:L.487 Hydrogen bonds: C:Q.383 Salt bridges: C:R.382 REA.20: 12 residues within 4Å: Chain A: R.382, Q.383 Chain B: A.337, Y.339, Y.343, F.348, F.351, L.361, F.366, C.406, L.487, F.489 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:A.337, B:Y.339, B:Y.339, B:Y.343, B:F.351, B:F.351, B:L.361, B:F.366, B:L.487, B:F.489 Hydrogen bonds: A:Q.383 Salt bridges: A:R.382 REA.30: 14 residues within 4Å: Chain B: Q.383 Chain C: F.312, A.337, Y.339, L.342, Y.343, A.346, F.348, F.351, L.361, F.366, C.406, I.408, L.487 14 PLIP interactions: 12 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.312, C:A.337, C:Y.339, C:L.342, C:Y.343, C:F.348, C:F.348, C:F.351, C:F.366, C:I.408, C:L.487 Hydrogen bonds: C:F.348, B:R.382, B:Q.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tong, L. et al., A Retinol Derivative Inhibits SARS-CoV-2 Infection by Interrupting Spike-Mediated Cellular Entry. Mbio (2022)

Release Date

2022-07-06

Peptides

Spike glycoprotein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

Spike glycoprotein