SMTL ID : 6ghv.5 (5 other biounits)

Structure of a DC-SIGN CRD in complex with high affinity glycomimetic.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: Q.57, R.60 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: F.13, F.14, Q.15 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: F.20, S.22, N.23, S.24 Ligand excluded by PLIP

1 x EZ8: [1-[(2~{S},3~{S},4~{R},5~{S},6~{R})-2-[(1~{S},2~{S},4~{S},5~{S})-2-(2-chloroethyloxy)-4,5-bis[[4-(hydroxymethyl)phenyl]methylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-1,2,3-triazol-4-yl]methylazanium(Non-covalent)

EZ8.3: 14 residues within 4Å: Chain A: F.64, E.98, N.100, V.102, G.103, E.105, E.109, S.111, N.116, D.117, D.118, K.119, K.124 Ligands: CA.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.102, A:V.102 Hydrogen bonds: A:E.98, A:N.100, A:E.105, A:E.109, A:S.111, A:N.116, A:K.119 Water bridges: A:G.103, A:D.118

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: E.98, N.100, E.105, N.116, D.117 Ligands: EZ8.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.98, A:E.105, A:D.117, A:D.117 CA.5: 5 residues within 4Å: Chain A: D.71, E.75, N.101, E.105, D.106 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.71, A:D.71, A:E.75, A:E.105, A:D.106 CA.6: 2 residues within 4Å: Chain A: E.75, D.106 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.106, H2O.1, H2O.1, H2O.2, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Medve, L. et al., Enhancing Potency and Selectivity of a DC-SIGN Glycomimetic Ligand by Fragment-Based Design: Structural Basis. Chemistry (2019)

Release Date

2019-09-11

Peptides

CD209 antigen: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

CD209 antigen

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