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

Structure of the A type blood alpha-D-galactosamine galactosaminidase D463A mutant from Flavonifractor plautii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 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 MN: MANGANESE (II) ION(Non-covalent)

MN.2: 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.7

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

CL.3: 5 residues within 4Å: Chain A: T.164, L.165, Q.512, R.515, R.516 Ligand excluded by PLIP

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 8 residues within 4Å: Chain A: D.320, W.361, K.435, A.437, Y.438, C.487, D.506, H.534 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.361, A:K.435, A:D.506 Water bridges: A:D.506 EDO.5: 4 residues within 4Å: Chain A: M.410, A.411, D.412, H.450 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.412, A:D.412 Water bridges: A:G.413 EDO.6: 7 residues within 4Å: Chain A: K.305, E.308, L.309, A.312, K.560, Y.563, E.564 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.305, A:K.305, A:E.308, A:E.308, A:E.564 EDO.7: 5 residues within 4Å: Chain A: A.390, R.391, P.393, G.398, P.443 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.391 Water bridges: A:G.398

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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