SMTL ID : 6w12.2 (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

homo-dimer

Ligands

12 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: 3 residues within 4Å: Chain A: H.18 Chain B: H.18 Ligands: CA.19 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.18, H2O.4, H2O.7 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 CA.15: 6 residues within 4Å: Chain B: Q.88, D.90, E.101, N.113, D.114 Ligands: A2G.28 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.90, B:E.101, B:D.114, B:D.114 CA.16: 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.126, B:E.126, H2O.7 CA.17: 2 residues within 4Å: Chain B: K.85, H.107 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.107, H2O.8, H2O.8, H2O.8 CA.18: 1 residues within 4Å: Chain B: H.9 No protein-ligand interaction detected (PLIP) CA.19: 3 residues within 4Å: Chain A: H.18 Chain B: H.18 Ligands: CA.5 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.18, H2O.3, H2O.8 CA.20: 4 residues within 4Å: Chain B: D.64, D.91, E.101, D.102 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.64, B:D.64, B:D.91, H2O.6, H2O.7

10 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 CL.21: 2 residues within 4Å: Chain B: R.119, P.120 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: Q.82, N.83, W.84 Ligand excluded by PLIP CL.23: 7 residues within 4Å: Chain B: S.12, H.36, E.126, A.127, G.128 Ligands: CL.24, ZN.26 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: H.36, G.128 Ligands: CL.23, ZN.26 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain B: E.101, D.102, V.116, C.117 Ligand excluded by PLIP

2 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 ZN.26: 3 residues within 4Å: Chain B: H.36 Ligands: CL.23, CL.24 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.36, H2O.5

2 x SER: SERINE(Non-covalent)

SER.13: 2 residues within 4Å: Chain A: W.92 Ligands: A2G.14 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:R.119, A:R.119 Hydrogen bonds: S.13, S.13 SER.27: 2 residues within 4Å: Chain B: W.92 Ligands: A2G.28 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Ligand interactions Water bridges: B:R.119, B:R.119 Hydrogen bonds: S.27, S.27

2 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 A2G.28: 12 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.15, SER.27 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.57 Hydrogen bonds: B:Q.88, B:E.101, B:N.113, B:D.115 Water bridges: B:E.101, S.27, S.27

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: 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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