SMTL ID : 7nl7.1

Crystal Structure of DC-SIGN in complex with a triazole-based glycomimetic ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.75, E.79, W.82, N.105, E.109, D.110 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.75, A:D.75, A:E.109, A:D.110, H2O.1 CA.2: 6 residues within 4Å: Chain A: E.102, N.104, E.109, N.120, D.121 Ligands: UH5.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.102, A:E.109, A:D.121, A:D.121 CA.3: 2 residues within 4Å: Chain A: E.79, D.110 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.110, H2O.1, H2O.1, H2O.1, H2O.2, H2O.4

1 x UH5: 3-Aminopropyl 2-deoxy-2-(4-phenyl-1,2,3-triazol-1-yl)-alpha-D-mannopyranoside(Non-covalent)

UH5.4: 12 residues within 4Å: Chain A: F.68, E.102, N.104, V.106, E.109, E.113, S.115, N.120, D.121, D.122, K.128 Ligands: CA.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.104, A:N.104, A:S.115, A:N.120, A:D.122 Water bridges: A:E.109, A:D.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cramer, J. et al., Sweet Drugs for Bad Bugs: A Glycomimetic Strategy against the DC-SIGN-Mediated Dissemination of SARS-CoV-2. J.Am.Chem.Soc. (2021)

Release Date

2021-10-27

Peptides

DC-SIGN, CRD domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DC-SIGN, CRD domain