SMTL ID : 9c44.1

SARS-CoV-2 S + S2L20

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

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.1: 1 residues within 4Å: Chain A: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.922 NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain D: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.922 NAG-NAG.8: 3 residues within 4Å: Chain D: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 1 residues within 4Å: Chain G: N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain G: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:L.922 NAG-NAG.12: 3 residues within 4Å: Chain G: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP)

3 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 A: N.234 Chain B: R.103, Y.104 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain D: N.234 Chain E: R.103, Y.104 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain G: N.234 Chain H: R.103, Y.104 No protein-ligand interaction detected (PLIP)

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

NAG.13: 4 residues within 4Å: Chain A: F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.280, N.282 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: Q.115, N.165 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.603, T.604 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.616, T.618 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: H.655, N.657 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain D: F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.280, N.282 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: Q.115, N.165 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: N.603, T.604 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.616, T.618 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: H.655, N.657 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain D: N.709, G.1131 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain D: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain D: N.1134 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain G: F.59, S.60, N.61, P.631 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain G: N.280, N.282 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: Q.115, N.165 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain G: N.603, T.604 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain G: N.616, T.618 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain G: H.655, N.657 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: N.709, G.1131 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain G: A.706, E.1072, K.1073, N.1074 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: N.1098, H.1101, F.1103 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain G: N.1134 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: N.331, P.579, Q.580 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, P. et al., Design of customized coronavirus receptors. Nature (2024)

Release Date

2024-11-20

Peptides

Spike glycoprotein: ADG
S2L20 Fab Heavy Chain Variable: BEH
S2L20 Fab Light Chain Variable Region: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
H

E
E

H
F

C
L

F
D

I
G

Spike glycoprotein

S2L20 Fab Heavy Chain Variable

S2L20 Fab Light Chain Variable Region

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