SMTL ID : 8c1v.1

SARS-CoV-2 S-trimer (3 RBDs up) bound to TriSb92, fitted into cryo-EM map

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG-NAG.1: 2 residues within 4Å: Chain C: D.1102, N.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: N.692, L.897, Q.1046 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain B: N.1109 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: N.692, L.897, Q.901, Q.1046 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.692, L.897, Q.1046 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 1 residues within 4Å: Chain A: N.1109 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.306, Q.555 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.1073, T.1075, H.1076, F.1078 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.255, N.257 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.632 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.591 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.776, S.778 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: N.684, G.1106 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: A.681, N.1049 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: Y.3, N.36 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: I.208, N.209 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.578 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.140 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: F.313, G.314, F.317, N.318 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.306 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain B: N.1073, T.1075, H.1076, F.1078 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: N.255, E.256, N.257 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.632 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.591 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.776 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.684, G.1106 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: A.681, N.1049 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain B: Y.3, N.36 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: I.208, N.209 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain B: N.578 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain B: N.140 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain B: F.313, G.314, F.317, N.318 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.306, Q.555 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain C: N.1073, T.1075, H.1076, F.1078 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain C: N.255, N.257 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.632 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.591, T.593 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.776 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.684, G.1106 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: A.681, N.1049 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: Y.3, N.36 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: I.208, N.209 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.578, T.579 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.140 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: F.313, G.314, F.317, N.318 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makela, A.R. et al., Intranasal trimeric sherpabody inhibits SARS-CoV-2 including recent immunoevasive Omicron subvariants. Nat Commun (2023)

Release Date

2023-04-19

Peptides

Spike glycoprotein: ABC
Sb92: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

E
E

F
F

Spike glycoprotein

Sb92