SMTL ID : 7p79.1

SARS-CoV-2 spike protein in complex with sybodyb#15 in a 1up/1up-out/1down conformation.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

4 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.1: 3 residues within 4Å: Chain C: N.717, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain B: N.717, L.922 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.922 NAG-NAG-BMA.13: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 No protein-ligand interaction detected (PLIP)

8 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)(Non-covalent)

NAG-NAG.2: 2 residues within 4Å: Chain C: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP)

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

NAG-BMA.10: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.1100, B:T.1100, B:H.1101 NAG-BMA.15: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.1101, C:N.1098, C:H.1101 NAG-BMA.16: 3 residues within 4Å: Chain A: N.1098, T.1100, H.1101 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.1101, A:N.1098, A:N.1098

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.12: 4 residues within 4Å: Chain A: K.558 Chain B: N.280, E.281, N.282 No protein-ligand interaction detected (PLIP)

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

NAG.17: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: N.709, I.1130 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: G.232, I.233, N.234 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.165 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain A: F.342, N.343, L.368, S.371, S.373, F.374, W.436 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.1074, T.1076 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: Y.28, F.59, N.61, P.631 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain B: G.232, I.233, N.234 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: F.342, N.343, L.368 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: K.1073, N.1074, T.1076 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walter, J.D. et al., Biparatopic sybodies neutralize SARS-CoV-2 variants of concern and mitigate drug resistance. Embo Rep. (2022)

Release Date

2021-08-04

Peptides

Spike glycoprotein: ABC
sybody#15: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
A

D
B

E
D

F
H

Spike glycoprotein

sybody#15

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