SMTL ID : 9emr.3 (2 other biounits)

Crystal Structure of DC-SIGN in complex with AL90

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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:E.79, H2O.1 CA.2: 7 residues within 4Å: Chain A: E.102, N.104, 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: 4 residues within 4Å: Chain A: E.79, E.108, D.110 Ligands: CA.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.79, A:E.108, A:D.110, H2O.1, H2O.4

1 x 01: (2~{R},3~{S},4~{R},5~{S},6~{S})-6-[(2~{S})-2,3-bis(oxidanyl)propoxy]-2-(hydroxymethyl)-5-(4-phenyl-1,2,3-triazol-1-yl)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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.104, A:N.104, A:E.109, A:S.115, A:N.120, A:N.120, A:K.123

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
C

DC-SIGN, CRD domain

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