SMTL ID : 4zrv.4 (3 other biounits)

Structure of cow mincle CRD complexed with trehalose mono butyrate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-trimer

Ligands

3 x GLC- U8V: 6-O-butanoyl-alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose(Non-covalent)

GLC-U8V.1: 9 residues within 4Å: Chain A: E.58, E.91, N.93, E.99, R.105, N.115, D.116, F.121 Ligands: CA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.58, A:R.105, A:N.115, A:E.91, A:N.93, A:E.99, A:R.105, A:R.105, A:N.115 Salt bridges: A:R.105 GLC-U8V.2: 14 residues within 4Å: Chain B: E.91, N.93, L.95, E.99, R.105, N.115, D.116, V.117, F.121 Chain C: F.120, F.121, N.122 Ligands: CA.8, ACT.11 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Water bridges: B:E.58, B:E.58, B:R.105, B:E.91 Hydrogen bonds: C:N.122, B:E.91, B:N.93, B:R.105, B:N.115, B:N.115 GLC-U8V.3: 13 residues within 4Å: Chain B: F.120, F.121 Chain C: E.58, E.91, N.93, L.95, E.99, R.105, N.115, D.116, V.117, F.121 Ligands: CA.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.58, C:E.58, C:R.105, C:N.115, C:E.91, C:N.93, C:E.99, C:R.105, C:R.105, C:N.115 Hydrophobic interactions: C:L.95 Salt bridges: C:R.105

9 x CA: CALCIUM ION(Non-covalent)

CA.4: 6 residues within 4Å: Chain A: E.91, N.93, E.99, N.115, D.116 Ligands: GLC-U8V.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.91, A:E.99, A:D.116, A:D.116 CA.5: 4 residues within 4Å: Chain A: V.39, N.41, E.45, E.128 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.39, A:E.45, A:E.128, A:E.128, H2O.4 CA.6: 6 residues within 4Å: Chain A: D.65, E.69, N.94, E.99, D.100 Ligands: ACT.7 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.65, A:D.65, A:E.69, A:E.99, A:D.100 CA.8: 6 residues within 4Å: Chain B: E.91, N.93, E.99, N.115, D.116 Ligands: GLC-U8V.2 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.91, B:E.99, B:D.116, B:D.116 CA.9: 4 residues within 4Å: Chain B: V.39, N.41, E.45, E.128 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.39, B:E.45, B:E.128, B:E.128, H2O.9 CA.10: 5 residues within 4Å: Chain B: D.65, E.69, N.94, E.99, D.100 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.65, B:D.65, B:E.69, B:D.100, H2O.7 CA.12: 6 residues within 4Å: Chain C: E.91, N.93, E.99, N.115, D.116 Ligands: GLC-U8V.3 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.91, C:E.99, C:D.116, C:D.116 CA.13: 4 residues within 4Å: Chain C: V.39, N.41, E.45, E.128 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.45, C:E.45, C:E.128, C:E.128, H2O.12 CA.14: 6 residues within 4Å: Chain C: D.65, E.69, N.94, E.99, D.100 Ligands: ACT.15 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.65, C:D.65, C:E.69, C:D.100, H2O.12

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 7 residues within 4Å: Chain A: D.65, Q.66, E.69, N.94, T.97, D.100 Ligands: CA.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.69 Water bridges: A:E.69, A:N.94, A:N.94 ACT.11: 4 residues within 4Å: Chain B: F.121 Chain C: F.121, N.122 Ligands: GLC-U8V.2 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.121 Hydrogen bonds: C:N.122, C:N.122 ACT.15: 6 residues within 4Å: Chain C: D.65, E.69, N.94, T.97, D.100 Ligands: CA.14 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.69, C:T.97 Water bridges: C:N.94, C:N.94

Links

RCSB   PDBe   PDBe-KB   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

2016-05-25

Peptides

Mincle CRD: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Mincle CRD

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