SMTL ID : 8r9w.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

9 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: Q.765, G.768, N.769 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 9 residues within 4Å: Chain A: V.278, S.407, S.408, V.409, F.451, N.453, T.455, T.456, L.460 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 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 NAG-NAG.6: 3 residues within 4Å: Chain H: Q.765, G.768, N.769 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 9 residues within 4Å: Chain H: V.278, S.407, S.408, V.409, F.451, N.453, T.455, T.456, L.460 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 8 residues within 4Å: Chain H: L.53, T.54, N.55, Y.182, T.184, Q.186, Y.188, L.223 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Q.186 NAG-NAG.11: 3 residues within 4Å: Chain I: Q.765, G.768, N.769 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 9 residues within 4Å: Chain I: V.278, S.407, S.408, V.409, F.451, N.453, T.455, T.456, L.460 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 8 residues within 4Å: Chain I: L.53, T.54, N.55, Y.182, T.184, Q.186, Y.188, L.223 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.186

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: 8 residues within 4Å: Chain A: Q.538, N.539, T.540, R.541, I.544, E.786, N.895, P.919 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.544 Hydrogen bonds: A:Q.538, A:R.541, A:N.539 NAG-NAG-BMA.7: 8 residues within 4Å: Chain H: Q.538, N.539, T.540, R.541, I.544, E.786, N.895, P.919 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.544 Hydrogen bonds: H:Q.538, H:R.541, H:N.539 NAG-NAG-BMA.12: 8 residues within 4Å: Chain I: Q.538, N.539, T.540, R.541, I.544, E.786, N.895, P.919 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:I.544 Hydrogen bonds: I:Q.538, I:R.541, I:N.539

3 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.4: 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 NAG-NAG-BMA-MAN-MAN.9: 9 residues within 4Å: Chain H: 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 H Hydrogen bonds: H:Q.105, H:T.106 NAG-NAG-BMA-MAN-MAN.14: 9 residues within 4Å: Chain I: 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 I Hydrogen bonds: I:Q.105, I:T.106

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

NAG.16: 4 residues within 4Å: Chain A: Q.290, N.292, G.311, N.327 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.633, T.648, R.650 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: E.551, R.924, N.926 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.475 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain A: V.478, F.493, T.494, N.507 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: V.980, F.982, Y.983, N.984 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: N.642, S.644 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.143, T.146 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain A: T.79, N.80, Y.95 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.133, L.148, N.165 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: T.231, N.232, M.684 Chain H: L.433 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain H: Q.290, N.292, G.311, N.327 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain H: N.633, T.648, R.650 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain H: E.551, R.924, N.926 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain H: N.475 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain H: V.478, F.493, T.494, N.507 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain H: V.980, F.982, Y.983, N.984 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain H: N.642, S.644 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain H: N.143, T.146 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain H: T.79, N.80, Y.95 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain H: N.133, L.148, N.165 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain H: T.231, N.232, M.684 Chain I: L.433 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain I: Q.290, N.292, G.311, N.327 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain I: N.633, T.648, R.650 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain I: E.551, R.924, N.926 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain I: N.475 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain I: V.478, F.493, T.494, N.507 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain I: V.980, F.982, Y.983, N.984 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain I: N.642, S.644 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain I: N.143, T.146 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain I: T.79, N.80, Y.95 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain I: N.133, L.148, N.165 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain A: L.433 Chain I: T.231, N.232, M.684 Ligand excluded by PLIP

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

Spike protein: AHI
22C10 antibody heavy chain: BDF
22C10 antibody light chain: CEG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
B

I
C

B
H

D
D

F
E

C
L

E
F

G
G

Spike protein

22C10 antibody heavy chain

22C10 antibody light chain

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