SMTL ID : 7n5h.1

Cryo-EM structure of broadly neutralizing antibody 2-36 in complex with prefusion SARS-CoV-2 spike glycoprotein

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

16 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: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 1 residues within 4Å: Chain A: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.717, L.922, Q.926 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.331, P.579, Q.580 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: I.1132, N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain B: N.717, L.922, Q.926 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.926 NAG-NAG.9: 3 residues within 4Å: Chain B: A.706, N.1074 Chain C: Q.895 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain B: N.331, P.579, Q.580, L.582 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain C: N.1134 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain C: N.717, T.719, L.922, Q.926, Q.1071 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: N.801, S.803, Q.804 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: N.331, Q.580, L.582 No protein-ligand interaction detected (PLIP)

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

NAG.17: 4 residues within 4Å: Chain A: A.706, E.1072, K.1073, N.1074 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1074 NAG.18: 2 residues within 4Å: Chain A: N.709, G.1131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.709 NAG.19: 2 residues within 4Å: Chain A: N.616, T.618 No protein-ligand interaction detected (PLIP) NAG.20: 1 residues within 4Å: Chain A: N.657 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.657 NAG.21: 4 residues within 4Å: Chain B: N.709, N.710, G.1131 Chain C: D.796 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.710 Hydrogen bonds: B:N.709 NAG.22: 3 residues within 4Å: Chain B: N.280, E.281, N.282 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.280, B:E.281 NAG.23: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.1074 NAG.24: 2 residues within 4Å: Chain C: H.655, N.657 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.655 NAG.25: 3 residues within 4Å: Chain A: D.796 Chain C: N.709, G.1131 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.709

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, P. et al., A monoclonal antibody that neutralizes SARS-CoV-2 variants, SARS-CoV, and other sarbecoviruses. Emerg Microbes Infect (2022)

Release Date

2021-11-03

Peptides

Spike glycoprotein: ABC
2-36 Fab heavy chain: DFH
2-36 Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

F
E

H
J

E
L

G
F

I
K

Spike glycoprotein

2-36 Fab heavy chain

2-36 Fab light chain

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