SMTL ID : 9ks7.1 (1 other biounit)

Crystal structure of T. rubripes Mincle with glycerol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: E.102, N.104, Y.106, R.109, E.111, K.122, N.126, D.127, L.128 Ligands: CA.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.104, A:N.104, A:R.109, A:E.111, A:N.126 Water bridges: A:E.102 GOL.4: 8 residues within 4Å: Chain B: E.102, N.104, Y.106, E.111, N.126, D.127, L.128 Ligands: CA.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.104, B:E.111, B:N.126, B:N.126

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: I.55, N.57, E.61, E.139 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.55, A:E.61, A:E.139, A:E.139, H2O.2 CA.3: 6 residues within 4Å: Chain A: E.102, N.104, E.111, N.126, D.127 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.102, A:E.111, A:D.127, A:D.127 CA.5: 4 residues within 4Å: Chain B: I.55, N.57, E.61, E.139 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.61, B:E.61, B:E.139, B:E.139, H2O.7 CA.6: 6 residues within 4Å: Chain B: E.102, N.104, E.111, N.126, D.127 Ligands: GOL.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.102, B:E.111, B:D.127, B:D.127

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ito, T. et al., Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates. Immunogenetics (2025)

Release Date

2025-04-02

Peptides

C-type lectin domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C-type lectin domain-containing protein

Related Entries With Identical Sequence