SMTL ID : 7tyz.1

Cryo-EM structure of SARS-CoV-2 spike in complex with FSR22, an anti-SARS-CoV-2 DARPin

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 3 residues within 4Å: Chain A: N.318, Q.567, L.569 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.12: 3 residues within 4Å: Chain C: N.318, I.319, Q.567 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 2 residues within 4Å: Chain E: N.318, Q.567 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 2 residues within 4Å: Chain A: N.696, G.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: G.326, E.327, N.330, A.359 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.359 NAG-NAG.7: 2 residues within 4Å: Chain C: N.696, G.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: E.327, N.330, A.359 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.359 NAG-NAG.14: 2 residues within 4Å: Chain E: N.696, G.1118 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain E: E.268, N.269 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain E: N.330, A.359 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:A.359

6 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 3 residues within 4Å: Chain A: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 1 residues within 4Å: Chain A: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 3 residues within 4Å: Chain C: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 1 residues within 4Å: Chain C: N.1121 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain E: N.788, S.790, Q.791 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 1 residues within 4Å: Chain E: N.1121 No protein-ligand interaction detected (PLIP)

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

NAG.19: 1 residues within 4Å: Chain A: N.48 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.590 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.603, T.605 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: A.693, N.1061 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: I.220, N.221 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: E.119, N.152 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.17, N.48 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain C: N.590 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.603, T.605 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: A.693, N.1061 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: G.219, I.220, N.221 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.152 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain E: Y.15, N.48 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain E: N.590 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: N.603, T.605 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain E: A.693, N.1061 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain E: N.221 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain E: N.152 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chonira, V. et al., A potent and broad neutralization of SARS-CoV-2 variants of concern by DARPins. Nat.Chem.Biol. (2023)

Release Date

2022-12-07

Peptides

Spike glycoprotein: ACE
DARPin FSR22: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Spike glycoprotein

DARPin FSR22

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