SMTL ID : 8sak.1

BtCoV-422 in complex with neutralizing antibody JC57-11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-mer

Ligands

12 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: 3 residues within 4Å: Chain A: N.52, S.54, K.55 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: D.20, S.21, G.22, W.185, N.226, L.229, I.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.22, A:I.244 NAG-NAG.4: 2 residues within 4Å: Chain A: N.866, T.868 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain B: N.52, K.55 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: D.20, S.21, G.22, W.185, N.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.20, B:D.20 NAG-NAG.7: 3 residues within 4Å: Chain A: K.505 Chain B: N.414, K.417 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain B: N.866, T.868, L.869 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain B: S.772, V.1207, F.1209, N.1211 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.52, S.54, K.55 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 8 residues within 4Å: Chain C: V.19, D.20, S.21, G.22, N.226, L.229, K.233, I.244 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.19, C:I.244 NAG-NAG.15: 3 residues within 4Å: Chain C: N.866, T.868, L.869 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain C: V.1207, F.1209, N.1211 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 4 residues within 4Å: Chain A: N.623, C.624, T.625, N.651 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.651, A:C.624, A:T.625 NAG-NAG-FUC.8: 3 residues within 4Å: Chain B: N.623, C.624, T.625 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.14: 3 residues within 4Å: Chain C: N.623, C.624, N.651 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.12: 7 residues within 4Å: Chain B: K.531, N.532, F.533, P.535 Chain C: N.170 Chain D: Y.104, S.106 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.106, D:S.106

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

NAG.17: 1 residues within 4Å: Chain A: N.37 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: N.69, V.333 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.159, G.163 Chain C: S.550, Q.551 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: F.169, N.170 Chain C: N.532, P.535 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain A: N.240 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.248 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.414, M.591 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: Q.713, N.724, L.755 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: V.1207, F.1209, N.1211 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain B: N.69, V.333 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.159, S.165 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: N.532, P.535 Chain B: N.170 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.248 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: L.712, Q.713, N.724 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: N.69, V.333 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain C: N.159 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.240 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain C: L.712, Q.713, N.724 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tse, L.V. et al., A MERS-CoV antibody neutralizes a pre-emerging group 2c bat coronavirus. Sci Transl Med (2023)

Release Date

2023-10-04

Peptides

Spike glycoprotein: ABC
JC57-11 Fab heavy chain: D
JC57-11 Fab light chain: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
H

E
L

Spike glycoprotein

JC57-11 Fab heavy chain

JC57-11 Fab light chain