SMTL ID : 6w12.1 (1 other biounit)

Crystal Structure of the Carbohydrate Recognition Domain of the Human Macrophage Galactose C-Type Lectin Bound to the Tumor-Associated Tn Antigen

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

6 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: Q.88, D.90, E.101, N.113, D.114 Ligands: A2G.14 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.90, A:E.101, A:D.114, A:D.114 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.126, A:E.126, H2O.3 CA.3: 2 residues within 4Å: Chain A: K.85, H.107 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.107, H2O.4, H2O.4, H2O.4 CA.4: 1 residues within 4Å: Chain A: H.9 No protein-ligand interaction detected (PLIP) CA.5: 1 residues within 4Å: Chain A: H.18 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.18, H2O.4 CA.6: 4 residues within 4Å: Chain A: D.64, D.91, E.101, D.102 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.64, A:D.64, A:D.91, H2O.2, H2O.3

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

CL.7: 2 residues within 4Å: Chain A: R.119, P.120 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: Q.82, N.83, W.84 Ligand excluded by PLIP CL.9: 7 residues within 4Å: Chain A: S.12, H.36, E.126, A.127, G.128 Ligands: CL.10, ZN.12 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: H.36, G.128 Ligands: CL.9, ZN.12 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain A: E.101, D.102, V.116, C.117 Ligand excluded by PLIP

1 x ZN: ZINC ION(Non-covalent)

ZN.12: 3 residues within 4Å: Chain A: H.36 Ligands: CL.9, CL.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.36, H2O.1

1 x SER: SERINE(Non-covalent)

SER.13: 2 residues within 4Å: Chain A: W.92 Ligands: A2G.14 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain A Hydrogen bonds: S.13, S.13 Water bridges: A:R.119, A:R.119

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

A2G.14: 12 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.1, SER.13 8 PLIP interactions: 5 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:Q.88, A:N.113, A:N.113, A:D.115 Water bridges: S.13, S.13, S.13

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

2021-03-10

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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