SMTL ID : 7byr.1

BD23-Fab in complex with the S ectodomain trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

5 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: 5 residues within 4Å: Chain A: N.717, L.922, N.925, Q.926, Q.1071 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.922 Hydrogen bonds: A:N.925 NAG-NAG.2: 2 residues within 4Å: Chain B: N.717, L.922 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain B: N.1098, T.1100, H.1101 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.1098, T.1100, H.1101, F.1103 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.717, L.922, N.925, Q.1071 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.925

1 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.6: 5 residues within 4Å: Chain B: Y.351 Chain C: N.164, N.165 Chain D: W.105, Y.106 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.616, Q.644 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.657 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.709, G.1131 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.801, S.803 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.1098, T.1100, H.1101, F.1103 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain A: V.1133, N.1134 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.122, N.125, V.171 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: E.132, N.165 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: T.108, N.234 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.282 Chain C: K.558 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: G.339, F.342, N.343 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.331, Q.580 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain B: N.616 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain B: N.657 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.709 Chain C: D.796 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.801, S.803 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain B: N.1134 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: K.558 Chain B: N.282 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain B: N.122, T.124, N.125, V.127, V.171 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: A.706, N.1074 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: F.338, G.339, F.342, N.343 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.1134 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: A.706, E.1072, N.1074 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.801, Q.804 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.709 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: H.655, N.657 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain C: N.616 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.603 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain B: R.457, N.460, E.465 Chain C: T.108, N.234, T.236 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain C: N.282 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: F.338, G.339, N.343 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cao, Y. et al., Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells. Cell (2020)

Release Date

2020-06-10

Peptides

Spike glycoprotein: ABC
Ab23-Fab-Heavy Chain: D
Ab23-Fab-Light Chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

Ab23-Fab-Heavy Chain

Ab23-Fab-Light Chain