SMTL ID : 7nl6.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.92, E.96, N.122, E.126, D.127 Ligands: CA.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.92, A:E.96, A:E.126, A:D.127, H2O.2 CA.2: 7 residues within 4Å: Chain A: E.119, N.121, V.123, E.126, N.137, D.138 Ligands: UH8.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.119, A:E.126, A:D.138, A:D.138 CA.3: 5 residues within 4Å: Chain A: E.96, N.122, E.125, D.127 Ligands: CA.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.96, A:E.125, A:D.127, A:D.127, H2O.1

1 x UH8: Methyl 2-deoxy-2-(4-(pyridine-3-yl))-1,2,3-triazol-1-yl)-alpha-D-mannopyranoside(Non-covalent)

UH8.4: 9 residues within 4Å: Chain A: E.119, N.121, V.123, E.126, N.137, D.138, D.139, K.140 Ligands: CA.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.121, A:N.121, A:E.126, A:N.137, A:K.140

1 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 5 residues within 4Å: Chain A: F.41, S.43, N.44, S.45, W.147 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.44, A:S.45, A:S.45, A:S.45

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