SMTL ID : 8ykg.1

Structure of SARS-CoV-2 spike glycoprotein in complex with NT-108 scFv (1-up state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-2-mer

Ligands

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.1: 3 residues within 4Å: Chain C: F.327, G.328, N.332 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain B: F.327, G.328, N.332 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: N.111, T.113, V.116 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.605, Q.633 Ligand excluded by PLIP NAG.5: 2 residues within 4Å: Chain A: N.698, G.1120 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.706 Ligand excluded by PLIP NAG.7: 2 residues within 4Å: Chain A: N.790, S.792 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: A.695, E.1061, K.1062, N.1063 Ligand excluded by PLIP NAG.9: 1 residues within 4Å: Chain A: N.1123 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: E.454 Chain B: T.97, N.223, T.225 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain B: N.605 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain B: N.698 Chain C: D.785 Ligand excluded by PLIP NAG.13: 2 residues within 4Å: Chain B: N.706, L.911 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain B: N.790, S.792, Q.793 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain B: N.1123 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: E.454 Chain C: T.97, N.223 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: N.320, Q.569 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: N.605, T.607 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain C: N.698 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain C: N.706, F.707, T.708, L.911, Q.915 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.790, S.792, Q.793 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anraku, Y. et al., Structural basis for potent neutralization activity of SARS-CoV-2 antibody, NT-108. To Be Published

Release Date

2025-03-12

Peptides

Spike glycoprotein: ABC
NT-108 scFv: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
F

Spike glycoprotein

NT-108 scFv

Related Entries With Identical Sequence