SMTL ID : 7lnp.1 (3 other biounits)

Structure of the exo-alpha-L-galactosidase BpGH29 (D264N mutant) from Bacteroides plebeius in complex with paranitrophenyl-alpha-L-galactopyranoside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.349, D.353, L.447, Y.502 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.349, A:D.353, A:L.447, A:Y.502, H2O.5

1 x Y9Y: paranitrophenyl-alpha-L-galactopyranoside(Non-covalent)

Y9Y.2: 15 residues within 4Å: Chain A: H.70, E.82, W.83, H.146, H.147, H.191, M.229, W.264, N.266, W.267, K.301, E.314, D.329, W.337, Y.419 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.83, A:W.267 Hydrogen bonds: A:W.83, A:H.146, A:H.191, A:N.266, A:K.301, A:D.329 Salt bridges: A:K.301

2 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 4 residues within 4Å: Chain A: W.449, K.498, Y.502, H.504 No protein-ligand interaction detected (PLIP) NI.4: 4 residues within 4Å: Chain A: K.334, S.347, H.350, K.425 No protein-ligand interaction detected (PLIP)

3 x NA: SODIUM ION(Non-functional Binders)

NA.5: 0 residues within 4Å: (No contacts) 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.453, A:S.453 NA.6: 3 residues within 4Å: Chain A: K.180, L.184, F.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.184, A:F.186 NA.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.8: 2 residues within 4Å: Chain A: K.61, R.403 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robb, C.S. et al., Metabolism of a hybrid algal galactan by members of the human gut microbiome. Nat.Chem.Biol. (2022)

Release Date

2022-02-09

Peptides

Exo-alpha-L-galactosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Exo-alpha-L-galactosidase

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