SMTL ID : 9emq.1

Crystal Structure of DC-SIGN in complex with AL86

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.75, E.79, N.105, E.109, D.110 Ligands: CA.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.75, A:D.75, A:E.79, A:D.110, H2O.1 CA.2: 8 residues within 4Å: Chain A: E.102, N.104, N.105, V.106, E.109, N.120, D.121 Ligands: 01.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.102, A:E.109, A:D.121, A:D.121 CA.3: 5 residues within 4Å: Chain A: E.79, N.105, E.108, D.110 Ligands: CA.1 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.79, A:E.108, H2O.1, H2O.3, H2O.4

1 x 01: (2~{R},3~{S},4~{R},5~{S},6~{S})-2-(hydroxymethyl)-5-(4-phenyl-1,2,3-triazol-1-yl)-6-[[(3~{S})-piperidin-3-yl]methoxy]oxane-3,4-diol

01.4: 13 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.123, K.128 Ligands: CA.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.68 Hydrogen bonds: A:N.104, A:N.104, A:E.109, A:E.109, A:E.113, A:N.120, A:K.123, A:K.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nemli, D.D. et al., Thermodynamics-Guided Design Reveals a Cooperative Hydrogen Bond in DC-SIGN-targeted Glycomimetics. J.Med.Chem. (2024)

Release Date

2024-11-13

Peptides

DC-SIGN, CRD domain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DC-SIGN, CRD domain

Related Entries With Identical Sequence