SMTL ID : 8r9x.1

Local refinement of the PDCoV spike glycoprotein ectodomain in complex with the 22C10 antibody Fab fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 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.1: 6 residues within 4Å: Chain A: T.79, N.80, Y.95 Chain C: S.31, D.32, D.50 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.31, C:S.31, C:D.50

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

NAG-NAG.2: 5 residues within 4Å: Chain A: E.125, N.133, V.135, L.148, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: L.53, T.54, N.55, Y.182, T.184, Q.186, Y.188, L.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.186

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.3: 9 residues within 4Å: Chain A: P.40, M.71, L.72, N.73, Y.104, Q.105, T.106, H.107, N.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.105, A:T.106

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

NAG.5: 3 residues within 4Å: Chain A: N.143, T.146 Ligands: NAG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.146 NAG.6: 4 residues within 4Å: Chain A: T.146, H.149, N.150 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.149 NAG.7: 2 residues within 4Å: Chain A: T.231, N.232 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.231 Hydrogen bonds: A:N.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Du, W. et al., Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein. Nat Commun (2024)

Release Date

2024-06-05

Peptides

PDCoV spike glycoprotein S1A domain: A
22C10 antibody heavy chain: B
22C10 antibody light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

PDCoV spike glycoprotein S1A domain

22C10 antibody heavy chain

22C10 antibody light chain

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