SMTL ID : 2xr6.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

2 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.1: 11 residues within 4Å: Chain A: E.113, N.115, V.117, E.120, N.131, D.132, D.133 Ligands: 07B.2, MAN.3, AE9.4, CA.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.115, A:E.120, A:N.131, A:N.131 Water bridges: A:N.131, A:D.133, A:D.133, A:D.133 MAN.3: 3 residues within 4Å: Ligands: MAN.1, 07B.2, AE9.4 No protein-ligand interaction detected (PLIP)

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.117 Ligands: MAN.1, MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.117

1 x AE9: 2-AZIDOETHANOL(Non-covalent)

AE9.4: 4 residues within 4Å: Chain A: N.115, V.117 Ligands: MAN.1, MAN.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.115

3 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: E.90, E.119, D.121 Ligands: CA.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.90, A:E.119, H2O.3, H2O.6, H2O.6 CA.6: 6 residues within 4Å: Chain A: D.86, E.90, N.116, E.120, D.121 Ligands: CA.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.86, A:D.86, A:E.120, A:D.121, H2O.6 CA.7: 6 residues within 4Å: Chain A: E.113, N.115, E.120, N.131, D.132 Ligands: MAN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.113, A:E.120, A:D.132, A:D.132

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

CL.8: 5 residues within 4Å: Chain A: E.119, E.120, D.121, K.134, C.135 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: P.21, C.22, F.28 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: K.51, Q.56 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sutkeviciute, I. et al., Unique Dc-Sign Clustering Activity of a Small Glycomimetic: A Lesson for Ligand Design. Acs Chem.Biol. (2014)

Release Date

2011-10-19

Peptides

CD209 ANTIGEN: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CD209 ANTIGEN