SMTL ID : 8vpf.1

Structure of SARS-CoV spike in complex with CoV1-65 Fab (NTD-bound)

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: R.1055, N.1080, F.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: I.1114, N.1116 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.699, Q.904, N.907, Q.908, K.911 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.904, A:N.907, A:Q.908 NAG-NAG.5: 3 residues within 4Å: Chain D: R.1055, N.1080, F.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain D: I.1114, N.1116 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: N.699, Q.904, N.907, Q.908, K.911 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Q.904, D:N.907, D:Q.908 NAG-NAG.9: 3 residues within 4Å: Chain G: R.1055, N.1080, F.1085 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain G: I.1114, N.1116 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain G: N.699, Q.904, N.907, Q.908, K.911 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:Q.904, G:N.907, G:Q.908

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.3: 5 residues within 4Å: Chain A: Y.778, N.783, S.785, Q.786, F.799 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.799 NAG-NAG-BMA.7: 5 residues within 4Å: Chain D: Y.778, N.783, S.785, Q.786, F.799 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.799 NAG-NAG-BMA.11: 5 residues within 4Å: Chain G: Y.778, N.783, S.785, Q.786, F.799 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.799

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

NAG.13: 4 residues within 4Å: Chain A: Q.32, N.65, Y.256, K.258 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.691, I.1112, G.1113 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain A: E.1054, N.1056 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: N.602, Q.630 Chain D: L.831 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: D.267, E.268, N.269 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain D: Q.32, N.65, Y.256, K.258 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: N.691, I.1112, G.1113 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain D: E.1054, N.1056 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain D: N.602, Q.630 Chain G: L.831 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain D: D.267, E.268, N.269 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain G: Q.32, N.65, Y.256, K.258 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain G: N.691, I.1112, G.1113 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain G: E.1054, N.1056 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: L.831 Chain G: N.602, Q.630 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain G: D.267, E.268, N.269 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suryadevara, N. et al., Structural characterization of human monoclonal antibodies targeting uncommon antigenic sites on spike glycoprotein of SARS-CoV. J.Clin.Invest. (2024)

Release Date

2025-03-19

Peptides

Spike glycoprotein: ADG
CoV1-65 antibody heavy chain: BEH
CoV1-65 antibody light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
M

E
D

H
E

C
N

F
F

I
G

Spike glycoprotein

CoV1-65 antibody heavy chain

CoV1-65 antibody light chain