SMTL ID : 6n1a.1

Crystal structure of an N-acetylgalactosamine deacetylase from F. plautii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: C.119, D.120, H.272 Ligands: GOL.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.120, A:H.272, H2O.3, H2O.5, H2O.8

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.213, D.216 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.213, A:D.213, A:D.216, A:D.216, H2O.10 CA.3: 3 residues within 4Å: Chain A: D.56, D.122, D.274 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.56, A:D.56, A:D.122, H2O.2, H2O.2

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: N.76, S.81, E.84, H.117, C.119, Y.335, W.387 Ligands: MN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.81, A:H.117 Water bridges: A:Y.335 GOL.5: 9 residues within 4Å: Chain A: K.31, A.32, P.33, G.34, G.324, P.325, S.328, W.329, D.330 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.31, A:A.32, A:G.34, A:S.328, A:D.330 GOL.6: 6 residues within 4Å: Chain A: Y.125, N.126, A.127, E.128, Y.211, F.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.125, A:A.127, A:E.128 Water bridges: A:N.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rahfeld, P. et al., An enzymatic pathway in the human gut microbiome that converts A to universal O type blood. Nat Microbiol (2019)

Release Date

2019-06-12

Peptides

Carbohydrate-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Carbohydrate-binding protein

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