SMTL ID : 2z8d.2 (2 other biounits)

The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-biose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x NAG- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-GAL.1: 14 residues within 4Å: Chain A: R.23, L.24, P.25, A.58, Q.79, D.128, E.177, N.180, W.231, W.252, G.288, G.289, S.290, L.323 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.79, A:G.289, A:S.290, A:S.290, A:R.23, A:R.23, A:E.177, A:N.180 Water bridges: A:R.23, A:R.23, A:R.23, A:S.290, A:A.58, A:Q.79, A:E.177, A:E.177

5 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: D.12, H.300, E.303 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.12, A:H.300, A:E.303 ZN.3: 2 residues within 4Å: Chain A: H.44, D.46 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.44, A:D.46, A:D.46, H2O.5, H2O.11 ZN.4: 3 residues within 4Å: Chain A: D.331, E.333 Ligands: ZN.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.331, A:E.333, H2O.9, H2O.17 ZN.5: 3 residues within 4Å: Chain A: D.331, E.333 Ligands: ZN.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.331, A:E.333, H2O.11 ZN.6: 1 residues within 4Å: Chain A: D.214 No protein-ligand interaction detected (PLIP)

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 4 residues within 4Å: Chain A: Q.103, Y.104, D.107, D.309 3 PLIP interactions: 3 interactions with chain A Water bridges: A:T.329 Salt bridges: A:D.107, A:D.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, R. et al., Structural and thermodynamic analyses of solute-binding Protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I. J.Biol.Chem. (2008)

Release Date

2008-03-18

Peptides

Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Galacto-N-biose/lacto-N-biose I transporter substrate-binding protein

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