SMTL ID : 9awt.2 (4 other biounits)

Structure of the A type blood alpha-D-galactosamine galactosaminidase from Flavonifractor plautii in complex with GalN-pNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.408, C.445, H.450, H.452 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.408, A:C.445, A:H.450, A:H.452

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

CL.2: 5 residues within 4Å: Chain A: T.164, L.165, Q.512, R.515, R.516 Ligand excluded by PLIP

1 x CO: COBALT (II) ION(Non-covalent)

CO.3: 5 residues within 4Å: Chain A: D.437, C.485, C.487, D.506 Ligands: 01.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.437, A:C.485, A:C.487

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.4: 4 residues within 4Å: Chain A: D.169, D.172, G.174, E.219 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.169, A:D.172, A:G.174, A:E.219, H2O.4

1 x 01: 4-nitrophenyl 2-amino-2-deoxy-alpha-D-galactopyranoside

01.5: 13 residues within 4Å: Chain A: M.159, W.291, D.320, D.321, W.361, N.400, K.435, D.437, Y.438, C.487, D.506, H.534 Ligands: CO.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.320, A:D.321, A:K.435, A:D.437 Water bridges: A:N.535 pi-Stacking: A:Y.438 pi-Cation interactions: A:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tian, Y. et al., Cobalt as a Cofactor for alpha-Galactosaminidase-Catalyzed Cleavage of Blood Group Antigens. Acs Catalysis (2024)

Release Date

2024-12-18

Peptides

A type blood alpha-D-galactosamine galactosaminidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

A type blood alpha-D-galactosamine galactosaminidase

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