SMTL ID : 5vyb.1

Structure of the carbohydrate recognition domain of Dectin-2 complexed with a mammalian-type high mannose Man9GlcNAc2 oligosaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose

BMA-MAN-MAN-MAN-MAN-MAN-MAN.1: 11 residues within 4Å: Chain A: S.73, E.106, N.108, E.112, V.118, W.120, N.128, D.129, V.130, R.136 Ligands: CA.2 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: E.106, N.108, E.112, N.128, D.129 Ligands: BMA-MAN-MAN-MAN-MAN-MAN-MAN.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.106, A:E.112, A:D.129, A:D.129 CA.3: 4 residues within 4Å: Chain A: V.54, N.56, E.60, E.141 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.54, A:E.60, A:E.141, H2O.1, H2O.1

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: W.87, H.109, E.112, D.129 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.109

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: F.101, W.102, T.123 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feinberg, H. et al., Mechanism of pathogen recognition by human dectin-2. J. Biol. Chem. (2017)

Release Date

2017-07-05

Peptides

C-type lectin domain family 6 member A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C-type lectin domain family 6 member A