SMTL ID : 6py1.1 (1 other biounit)

Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to GalNAc

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.1: 11 residues within 4Å: Chain A: Y.59, Q.90, D.92, W.94, E.103, H.107, H.109, N.115, D.116, D.117 Ligands: CA.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.59 Hydrogen bonds: A:Q.90, A:N.115 Water bridges: A:W.94, A:D.117, A:D.117

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

ACT.2: 4 residues within 4Å: Chain A: G.69, A.70, W.71, Y.79 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.70 Hydrogen bonds: A:W.71 Water bridges: A:Y.79

4 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: V.41, N.43, E.47, E.128 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:V.41, A:E.47, A:E.128, A:E.128, H2O.3 CA.4: 4 residues within 4Å: Chain A: D.66, D.93, E.103, D.104 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.66, A:D.66, A:D.93, A:D.104, H2O.3 CA.5: 6 residues within 4Å: Chain A: Q.90, D.92, E.103, N.115, D.116 Ligands: A2G.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.92, A:E.103, A:D.116, A:D.116 CA.6: 4 residues within 4Å: Chain A: E.29, Q.33, H.38, L.39 No protein-ligand interaction detected (PLIP)

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

CL.7: 2 residues within 4Å: Chain A: R.121, P.122 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: W.17, H.20, S.21 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: Q.84, N.85, W.86 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: D.104, D.117, V.118, C.119 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: W.94, Q.95 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

2020-07-29

Peptides

C-type lectin domain family 10 member A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C-type lectin domain family 10 member A

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