SMTL ID : 8elj.1

SARS-CoV-2 spike glycoprotein in complex with the ICO-hu23 neutralizing 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: 3 residues within 4Å: Chain A: N.724, L.929, Q.933 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.808, S.810 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.1105, T.1107, H.1108, F.1110 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 1 residues within 4Å: Chain A: N.1141 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.724, L.929, Q.933 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.808, S.810 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.1105, T.1107, H.1108, F.1110 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain B: N.1141 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.724, L.929, Q.933 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.808, S.810 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain C: N.1105, T.1107, H.1108, F.1110 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain C: N.1141 No protein-ligand interaction detected (PLIP)

30 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.13: 1 residues within 4Å: Chain A: N.68 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: N.129, A.130, N.132, V.134, K.136 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.287, E.288, N.289 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: P.337, N.338, P.586, Q.587 Ligand excluded by PLIP NAG.17: 7 residues within 4Å: Chain A: F.345, N.350, V.374, L.375, S.378, S.380, F.381 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain A: N.610 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain A: N.623 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: H.662, V.663, N.664 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.716, G.1138 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain A: E.1079, N.1081 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain B: N.68 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain B: N.129, A.130, N.132, V.134, K.136 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.287, E.288, N.289 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: P.337, N.338, P.586, Q.587 Ligand excluded by PLIP NAG.27: 7 residues within 4Å: Chain B: F.345, F.349, N.350, V.374, L.375, S.378, S.380 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.610 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.623 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: H.662, V.663, N.664 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.716, G.1138 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain B: E.1079, N.1081 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.68 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain C: N.129, A.130, N.132, V.134, K.136 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.287, E.288, N.289 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain C: P.337, N.338, P.586, Q.587 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain C: F.345, N.350, V.374, L.375, S.378, S.380 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.610 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.623 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: H.662, V.663, N.664 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.716, G.1138 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: E.1079, N.1081 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hermet, P. et al., Broadly neutralizing humanized SARS-CoV-2 antibody binds to a conserved epitope on Spike and provides antiviral protection through inhalation-based delivery in non-human primates. Plos Pathog. (2023)

Release Date

2023-07-19

Peptides

Spike glycoprotein: ABC
ICO-hu23 antibody Fab heavy chain: DFH
ICO-hu23 antibody Fab light chain: EGI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
S

F
U

H
W

E
T

G
V

I
X

Spike glycoprotein

ICO-hu23 antibody Fab heavy chain

ICO-hu23 antibody Fab light chain

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