SMTL ID : 7pnm.1

Human coronavirus OC43 spike glycoprotein ectodomain in complex with the 46C12 antibody Fab fragment

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-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: 2 residues within 4Å: Chain A: N.143, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: R.153, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: E.348, N.373, S.376, F.380, T.617 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.380 NAG-NAG.4: 4 residues within 4Å: Chain A: E.933, N.937, G.941, A.942 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain D: N.143, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain D: R.153, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain D: E.348, N.373, S.376, F.380, T.617 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.380 NAG-NAG.8: 4 residues within 4Å: Chain D: E.933, N.937, G.941, A.942 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain G: N.143, N.177 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain G: R.153, L.168, E.170, K.210, R.211, N.212 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain G: E.348, N.373, S.376, F.380, T.617 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.380 NAG-NAG.12: 4 residues within 4Å: Chain G: E.933, N.937, G.941, A.942 No protein-ligand interaction detected (PLIP)

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

NAG.13: 1 residues within 4Å: Chain A: N.451 Ligand excluded by PLIP NAG.14: 1 residues within 4Å: Chain A: N.649 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: F.727, D.728, N.739, T.741 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.69, Q.290 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain A: N.156, L.165 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: I.674, N.676 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: H.694, N.696 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.714 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain D: N.451 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain D: N.649 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain D: F.727, D.728, N.739, T.741 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain D: N.69, Q.290 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: N.156, L.165 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: I.674, N.676 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: H.694, N.696 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.714 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain G: N.451 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain G: N.649 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain G: F.727, D.728, N.739, T.741 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain G: N.69, Q.290 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain G: N.156, L.165 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain G: I.674, N.676 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain G: H.694, N.696 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain G: N.714 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, C. et al., Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes. Nat Commun (2022)

Release Date

2022-04-20

Peptides

Spike glycoprotein: ADG
46C12 antibody light chain: BEH
46C12 antibody heavy chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
C

B
L

E
D

H
E

C
H

F
G

I
I

Spike glycoprotein

46C12 antibody light chain

46C12 antibody heavy chain

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