SMTL ID : 7uaq.1

Structure of the SARS-CoV-2 NTD in complex with C1520, local refinement

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

3 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: 5 residues within 4Å: Chain A: N.122, N.125, V.127, E.154 Chain B: S.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.125 NAG-NAG.2: 5 residues within 4Å: Chain A: H.146, N.148, N.149, S.151, M.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.146 NAG-NAG.3: 2 residues within 4Å: Chain A: T.108, N.234 No protein-ligand interaction detected (PLIP)

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

NAG.4: 2 residues within 4Å: Chain A: Y.28, N.61 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.28 NAG.5: 1 residues within 4Å: Chain A: N.165 No protein-ligand interaction detected (PLIP) NAG.6: 2 residues within 4Å: Chain A: E.281, N.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.281, A:N.282 NAG.7: 4 residues within 4Å: Chain C: N.19, S.69, F.76, T.78 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins. Immunity (2022)

Release Date

2022-04-27

Peptides

Spike glycoprotein: A
C1520 Fab Heavy Chain: B
C1520 Fab Light Chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

Spike glycoprotein

C1520 Fab Heavy Chain

C1520 Fab Light Chain

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