SMTL ID : 7p78.1

SARS-CoV-2 spike protein in complex with sybody#15 and sybody#68 in a 1up/1up-out/1down conformation

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-mer

Ligands

11 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.1: 3 residues within 4Å: Chain C: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain A: N.801, S.803 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: N.331, Q.580, T.581 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 1 residues within 4Å: Chain B: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP)

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.2: 3 residues within 4Å: Chain C: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain B: N.717, L.922, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 2 residues within 4Å: Chain B: N.801, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 2 residues within 4Å: Chain B: N.331, Q.580 No protein-ligand interaction detected (PLIP)

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.13: 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: 1 residues within 4Å: Chain A: N.709 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: F.59, N.61 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: 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: 6 residues within 4Å: Chain A: F.342, L.368, S.371, S.373, F.374, W.436 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.1074, T.1076, S.1097, N.1098 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: 1 residues within 4Å: Chain B: N.709 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: 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: 2 residues within 4Å: Chain B: N.603, T.604 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: F.342, N.343 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain B: N.1074 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
sybody#68: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
E

C
A

D
B

E
D

F
H

G
W

H
Y

Spike glycoprotein

sybody#15

sybody#68

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