SMTL ID : 6xey.1

Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-4

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

7 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 A: N.481 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.926 NAG-NAG.5: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: N.717, L.922, Q.926, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.922 NAG-NAG.10: 5 residues within 4Å: Chain B: V.483 Chain D: T.58, N.59 Chain E: S.96, N.97 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 8 residues within 4Å: Chain A: V.483 Chain F: T.58, N.59, Y.60 Chain I: S.96, N.97 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: V.483 Chain G: T.58, N.59, Y.60 Chain H: N.97 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: 7 residues within 4Å: Chain A: F.338, G.339, F.342, N.343, V.367 Chain G: Y.106 Chain H: Y.34 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:Y.34, H:Y.34 NAG-NAG-BMA.6: 5 residues within 4Å: Chain B: F.338, G.339, N.343 Chain F: Y.106 Chain I: Y.34 3 PLIP interactions: 1 interactions with chain I, 2 interactions with chain F Hydrogen bonds: I:Y.34, F:Y.106, F:Y.106 NAG-NAG-BMA.7: 5 residues within 4Å: Chain C: F.338, G.339, N.343 Chain D: Y.106 Chain E: Y.34 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:Y.106, E:Y.34, E:Y.34

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

NAG-BMA.4: 1 residues within 4Å: Chain B: N.481 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.481 NAG-BMA.8: 1 residues within 4Å: Chain C: N.481 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: E.1072, N.1074 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: E.281, N.282 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.1134 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.1098, T.1100, F.1103 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.709, G.1131 Chain B: D.796 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.616 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.603 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.165, T.167 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain B: N.603 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain B: N.282 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain B: N.331, P.579, Q.580 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: T.108, N.234 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.709, G.1131 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.165 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.616, T.618 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.657 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain C: N.331, Q.580 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: T.108, N.234 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: E.1072, N.1074 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: S.112, E.132, N.165 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.616, Q.644 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.801 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: N.280, N.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, L. et al., Potent neutralizing antibodies against multiple epitopes on SARS-CoV-2 spike. Nature (2020)

Release Date

2020-07-22

Peptides

Spike glycoprotein: ABC
2-4 Heavy Chain: DFG
2-4 Light Chain: EHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

F
H

G
J

E
G

H
K

I
L

Spike glycoprotein

2-4 Heavy Chain

2-4 Light Chain

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