SMTL ID : 2xr5.1

Crystal structure of the complex of the carbohydrate recognition domain of human DC-SIGN with pseudo dimannoside mimic.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

monomer

Ligands

1 x MAN: alpha-D-mannopyranose(Non-covalent)

MAN.1: 10 residues within 4Å: Chain A: E.109, N.111, V.113, E.116, N.127, D.128, D.129 Ligands: 07B.2, ETA.3, CA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.111, A:E.116, A:N.127 Water bridges: A:N.127, A:N.127, A:D.129, A:D.129

1 x 07B: dimethyl (1S,2S,4S,5S)-4,5-dihydroxycyclohexane-1,2-dicarboxylate(Non-covalent)

07B.2: 3 residues within 4Å: Chain A: V.113 Ligands: MAN.1, ETA.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.113

1 x ETA: ETHANOLAMINE(Non-functional Binders)

ETA.3: 2 residues within 4Å: Ligands: MAN.1, 07B.2 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: E.109, N.111, E.116, N.127, D.128 Ligands: MAN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.109, A:E.116, A:D.128, A:D.128 CA.5: 6 residues within 4Å: Chain A: D.82, E.86, N.112, E.116, D.117 Ligands: CA.6 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.82, A:D.82, A:E.116, A:D.117, H2O.6 CA.6: 4 residues within 4Å: Chain A: E.86, E.115, D.117 Ligands: CA.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.86, A:E.115, H2O.3, H2O.6, H2O.6

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

CL.7: 2 residues within 4Å: Chain A: S.35, R.37 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: F.31, S.33, N.34, S.35 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: K.47, Q.52 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thepaut, M. et al., Structure of a Glycomimetic Ligand in the Carbohydrate Recognition Domain of C-Type Lectin Dc-Sign. Structural Requirements for Selectivity and Ligand Design. J.Am.Chem.Soc. (2013)

Release Date

2011-10-19

Peptides

CD209 ANTIGEN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CD209 ANTIGEN