SMTL ID : 6n1b.1

Crystal structure of an N-acetylgalactosamine deacetylase from F. plautii in complex with blood group B trisaccharide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

1 x GAL- FUC- GLA: alpha-L-fucopyranose-(1-2)-[alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose

GAL-FUC-GLA.1: 13 residues within 4Å: Chain A: R.79, S.81, H.117, C.119, D.141, Y.202, L.205, V.228, G.229, Y.230, W.271, Y.335 Ligands: CA.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:S.81, A:D.141, A:V.228, A:Y.230, A:Y.335 Water bridges: A:N.76, A:N.76, A:S.81, A:T.114, A:D.141, A:Y.202, A:N.76, A:Y.230, A:Y.230, A:Q.231, A:N.76, A:E.84, A:E.84, A:H.117, A:D.120, A:Q.231, A:Y.335

4 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 3 residues within 4Å: Chain A: D.120, H.272 Ligands: GAL-FUC-GLA.1 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.120, A:H.272, H2O.1, H2O.1, H2O.4, H2O.4 CA.3: 3 residues within 4Å: Chain A: D.56, D.122, D.274 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.56, A:D.56, H2O.1, H2O.3, H2O.3 CA.4: 1 residues within 4Å: Chain A: N.256 No protein-ligand interaction detected (PLIP) CA.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 6 residues within 4Å: Chain A: G.260, L.261, E.313, Q.314, G.316, T.317 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.261, A:G.316 Water bridges: A:Q.314 GOL.7: 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 GOL.8: 9 residues within 4Å: Chain A: K.31, A.32, P.33, G.34, G.324, S.328, W.329, D.330, Y.356 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.31, A:G.34, A:G.34, A:S.328, A:D.330 Water bridges: A:A.32

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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