SMTL ID : 5m62.1 (1 other biounit)

Structure of the Mus musclus Langerin carbohydrate recognition domain in complex with glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-trimer

Ligands

3 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: E.98, N.100, E.106, N.120, D.121 Ligands: BGC.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.98, A:E.106, A:D.121, A:D.121 CA.10: 6 residues within 4Å: Chain B: E.98, N.100, E.106, N.120, D.121 Ligands: BGC.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.98, B:E.106, B:D.121, B:D.121 CA.19: 6 residues within 4Å: Chain C: E.98, N.100, E.106, N.120, D.121 Ligands: BGC.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.98, C:E.106, C:D.121, C:D.121

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: G.61, S.114 Chain C: K.27, F.35 Ligand excluded by PLIP GOL.3: 7 residues within 4Å: Chain A: Y.21, S.23, R.24, T.25, K.27, F.35 Chain B: D.60 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: N.104, N.105, H.107 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: N.110, R.112, N.120, G.122, N.126, F.128 Ligands: BGC.9 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: W.77, F.85, K.87, S.90, R.91, W.94, P.99 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: R.10, S.38, R.39, R.134 Chain B: K.57 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: K.27, F.35 Chain B: G.61, S.114 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain B: Y.21, S.23, R.24, T.25, K.27, F.35 Chain C: D.60 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain B: N.104, N.105, H.107 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain B: N.110, R.112, N.120, G.122, N.126, F.128 Ligands: BGC.18 Ligand excluded by PLIP GOL.15: 7 residues within 4Å: Chain B: W.77, F.85, K.87, S.90, R.91, W.94, P.99 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: R.10, S.38, R.39, R.134 Chain C: K.57 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: K.27, F.35 Chain C: G.61, S.114 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain A: D.60 Chain C: Y.21, S.23, R.24, T.25, K.27, F.35 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain C: N.104, N.105, H.107 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain C: N.110, R.112, N.120, G.122, N.126, F.128 Ligands: BGC.27 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain C: W.77, F.85, K.87, S.90, R.91, W.94, P.99 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain A: K.57 Chain C: R.10, S.38, R.39, R.134 Ligand excluded by PLIP

3 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.8: 3 residues within 4Å: Chain A: N.126, T.127, F.128 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.126, A:T.127 Water bridges: A:N.126 P6G.17: 3 residues within 4Å: Chain B: N.126, T.127, F.128 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.126, B:T.127 Water bridges: B:N.126 P6G.26: 3 residues within 4Å: Chain C: N.126, T.127, F.128 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.126, C:T.127 Water bridges: C:N.126

3 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.9: 8 residues within 4Å: Chain A: E.98, N.100, E.106, R.112, N.120, D.121 Ligands: CA.1, GOL.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.98, A:N.100, A:R.112, A:R.112, A:N.120 Water bridges: A:E.106, A:N.126 BGC.18: 8 residues within 4Å: Chain B: E.98, N.100, E.106, R.112, N.120, D.121 Ligands: CA.10, GOL.14 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:E.98, B:N.100, B:R.112, B:R.112, B:N.120 Water bridges: B:E.98, B:E.98, B:E.106, B:E.106, B:N.126 BGC.27: 8 residues within 4Å: Chain C: E.98, N.100, E.106, R.112, N.120, D.121 Ligands: CA.19, GOL.23 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.98, C:N.100, C:R.112, C:R.112, C:N.120, C:N.120 Water bridges: C:E.98, C:E.98, C:E.106, C:E.106, C:N.126

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Hanske, J. et al., Bacterial Polysaccharide Specificity of the Pattern Recognition Receptor Langerin Is Highly Species-dependent. J. Biol. Chem. (2017)

Release Date

2016-12-07

Peptides

C-type lectin domain family 4 member K: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

C-type lectin domain family 4 member K

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