SMTL ID : 6xiy.1

Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to methyl 2-(acetylamino)-2-deoxy-1-thio-alpha-D-galactopyranose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

homo-dimer

Ligands

2 x Q3M: Methyl 2-(acetylamino)-2-deoxy-1-thio-alpha-D-galactopyranose(Non-covalent)

Q3M.1: 11 residues within 4Å: Chain A: Y.57, Q.88, D.90, W.92, E.101, H.105, H.107, N.113, D.114, D.115 Ligands: CA.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.57, A:W.92 Hydrogen bonds: A:Q.88, A:D.90, A:E.101, A:N.113 Water bridges: A:D.115 Q3M.12: 11 residues within 4Å: Chain B: Y.57, Q.88, D.90, W.92, E.101, H.105, H.107, N.113, D.114, D.115 Ligands: CA.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.57, B:W.92 Hydrogen bonds: B:Q.88, B:D.90, B:E.101, B:N.113 Water bridges: B:D.115

6 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: V.39, N.41, E.45, E.126 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.39, A:E.45, A:E.45, A:E.126, H2O.2 CA.3: 6 residues within 4Å: Chain A: Q.88, D.90, E.101, N.113, D.114 Ligands: Q3M.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.90, A:E.101, A:D.114, A:D.114 CA.4: 4 residues within 4Å: Chain A: D.64, D.91, E.101, D.102 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.64, A:D.91, A:E.101, A:D.102, H2O.1 CA.13: 4 residues within 4Å: Chain B: V.39, N.41, E.45, E.126 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.39, B:E.45, B:E.45, B:E.126, H2O.5 CA.14: 6 residues within 4Å: Chain B: Q.88, D.90, E.101, N.113, D.114 Ligands: Q3M.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.90, B:E.101, B:D.114, B:D.114 CA.15: 4 residues within 4Å: Chain B: D.64, D.91, E.101, D.102 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.64, B:D.91, B:E.101, B:D.102, H2O.5

14 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: W.92, Q.93 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain A: R.119, P.120 Chain B: R.119, P.120 Ligands: CL.17 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: W.15, H.18, S.19 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: D.102, V.116, C.117 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: A.68, W.69 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: K.85, H.107, P.108, D.109 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: Q.82, N.83, W.84 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: W.92, Q.93 Ligand excluded by PLIP CL.17: 5 residues within 4Å: Chain A: R.119, P.120 Chain B: R.119, P.120 Ligands: CL.6 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: W.15, H.18, S.19 Ligand excluded by PLIP CL.19: 3 residues within 4Å: Chain B: D.102, V.116, C.117 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: A.68, W.69 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: K.85, H.107, P.108, D.109 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: Q.82, N.83, W.84 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gabba, A. et al., Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to GalNAc and the Tumor-Associated Tn Antigen. Biochemistry (2021)

Release Date

2021-03-31

Peptides

C-type lectin domain family 10 member A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C-type lectin domain family 10 member A

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