SMTL ID : 5kth.1

Structure of cow mincle complexed with brartemicin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

monomer

Ligands

1 x GLC- GLC: alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 12 residues within 4Å: Chain A: E.73, E.106, N.108, L.110, E.114, R.120, N.130, D.131, F.136 Ligands: 6X7.2, 6X7.3, CA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.106, A:N.108, A:E.114, A:R.120, A:R.120, A:N.130 Salt bridges: A:R.120

2 x 6X7: 2,4-dihydroxy-6-methyl Benzoic acid(Non-covalent)(Non-functional Binders)

6X7.2: 5 residues within 4Å: Chain A: E.73, F.136 Ligands: GLC-GLC.1, GLC-GLC.1, PGE.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.136 6X7.3: 1 residues within 4Å: Ligands: GLC-GLC.1 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: E.106, N.108, E.114, N.130, D.131 Ligands: GLC-GLC.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.106, A:E.114, A:D.131, A:D.131 CA.5: 4 residues within 4Å: Chain A: V.54, N.56, E.60, E.143 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.60, A:E.60, A:E.143, A:E.143, H2O.1 CA.6: 5 residues within 4Å: Chain A: D.80, E.84, N.109, E.114, D.115 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.80, A:D.80, A:E.84, A:E.114, A:D.115

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.7: 3 residues within 4Å: Chain A: F.136, N.137 Ligands: 6X7.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Feinberg, H. et al., Binding Sites for Acylated Trehalose Analogs of Glycolipid Ligands on an Extended Carbohydrate Recognition Domain of the Macrophage Receptor Mincle. J.Biol.Chem. (2016)

Release Date

2016-08-31

Peptides

mincle protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

mincle protein

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