SMTL ID : 8rov.1

Human dectin-2 with dimerization domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.152, N.154, E.158, N.174, D.175 Ligands: MMA.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.152, A:E.158, A:D.175, A:D.175 CA.2: 4 residues within 4Å: Chain A: V.100, N.102, E.106, E.187 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:V.100, A:E.106, A:E.187, H2O.1, H2O.1 CA.5: 6 residues within 4Å: Chain B: E.152, N.154, E.158, N.174, D.175 Ligands: MMA.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.152, B:E.158, B:D.175, B:D.175 CA.6: 4 residues within 4Å: Chain B: V.100, N.102, E.106, E.187 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.100, B:E.106, B:E.187, B:E.187, H2O.1

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

NA.3: 4 residues within 4Å: Chain A: W.133, H.155, E.158, D.175 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.155 NA.7: 4 residues within 4Å: Chain B: W.133, H.155, E.158, D.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.158, B:D.175

2 x MMA: methyl alpha-D-mannopyranoside(Non-covalent)

MMA.4: 7 residues within 4Å: Chain A: E.152, N.154, E.158, W.166, N.174, D.175 Ligands: CA.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.154, A:E.158, A:N.174 Water bridges: A:E.158, A:R.182 MMA.8: 6 residues within 4Å: Chain B: E.152, N.154, E.158, N.174, D.175 Ligands: CA.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.154, B:E.158, B:N.174 Water bridges: B:E.158, B:R.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Interactions that define the arrangement of sugar-binding sites in BDCA-2 and dectin-2 dimers. Glycobiology (2024)

Release Date

2024-10-16

Peptides

C-type lectin domain family 6 member A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C-type lectin domain family 6 member A