SMTL ID : 2z8d.3 (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

homo-tetramer

Ligands

4 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 NAG-GAL.8: 14 residues within 4Å: Chain B: 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 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.79, B:G.289, B:S.290, B:S.290, B:R.23, B:R.23, B:E.177, B:N.180 Water bridges: B:R.23, B:R.23, B:R.23, B:S.290, B:A.58, B:Q.79 NAG-GAL.15: 14 residues within 4Å: Chain C: 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 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:Q.79, C:G.289, C:S.290, C:S.290, C:R.23, C:R.23, C:E.177, C:N.180 Water bridges: C:R.23, C:R.23, C:R.23, C:R.23, C:K.57, C:A.58, C:A.58, C:S.59, C:S.59, C:Q.79, C:E.177 NAG-GAL.19: 14 residues within 4Å: Chain D: 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 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Q.79, D:G.289, D:S.290, D:S.290, D:R.23, D:R.23, D:E.177, D:N.180 Water bridges: D:R.23, D:R.23, D:R.23, D:R.23, D:K.57, D:A.58, D:A.58, D:S.59, D:S.59, D:Q.79, D:E.177, D:E.177

14 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.12, H.300, E.303 Chain C: D.11 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Metal complexes: A:D.12, A:H.300, A:E.303, C:D.11 ZN.3: 3 residues within 4Å: Chain A: H.44, D.46 Chain C: E.306 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: 7 residues within 4Å: Chain A: D.331, E.333 Chain B: D.331, E.333 Ligands: ZN.5, ZN.11, ZN.12 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.331, A:E.333, B:E.333, H2O.9, H2O.27 ZN.5: 5 residues within 4Å: Chain A: D.331, E.333 Chain B: D.331 Ligands: ZN.4, ZN.11 6 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.331, A:D.331, A:E.333, H2O.11, H2O.35, H2O.36 ZN.6: 1 residues within 4Å: Chain A: D.214 No protein-ligand interaction detected (PLIP) ZN.9: 4 residues within 4Å: Chain B: D.12, H.300, E.303 Chain D: D.11 4 PLIP interactions: 1 interactions with chain D, 3 interactions with chain B Metal complexes: D:D.11, B:D.12, B:H.300, B:E.303 ZN.10: 3 residues within 4Å: Chain B: H.44, D.46 Chain D: E.306 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.44, B:D.46, B:D.46, H2O.24, H2O.29 ZN.11: 7 residues within 4Å: Chain A: D.331, E.333 Chain B: D.331, E.333 Ligands: ZN.4, ZN.5, ZN.12 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.331, B:E.333, A:E.333, H2O.9, H2O.27 ZN.12: 5 residues within 4Å: Chain A: D.331 Chain B: D.331, E.333 Ligands: ZN.4, ZN.11 6 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.331, B:E.333, A:D.331, H2O.17, H2O.17, H2O.29 ZN.13: 1 residues within 4Å: Chain B: D.214 No protein-ligand interaction detected (PLIP) ZN.16: 4 residues within 4Å: Chain A: D.11 Chain C: D.12, H.300, E.303 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:D.12, C:H.300, C:E.303, A:D.11, A:D.11 ZN.17: 3 residues within 4Å: Chain A: E.306 Chain C: H.44, D.46 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:E.306, A:E.306, C:H.44, C:D.46, H2O.41 ZN.20: 4 residues within 4Å: Chain B: D.11 Chain D: D.12, H.300, E.303 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain B Metal complexes: D:D.12, D:H.300, D:E.303, B:D.11, B:D.11 ZN.21: 3 residues within 4Å: Chain B: E.306 Chain D: H.44, D.46 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:H.44, D:D.46, B:E.306, B:E.306, H2O.59

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

MES.7: 7 residues within 4Å: Chain A: Q.103, Y.104, D.107, D.309 Chain C: K.42, Q.43, P.45 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Water bridges: A:T.329 Salt bridges: A:D.107, A:D.309, C:K.42 Hydrogen bonds: C:Q.43 MES.14: 7 residues within 4Å: Chain B: Q.103, Y.104, D.107, D.309 Chain D: K.42, Q.43, P.45 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: D:Q.43 Salt bridges: D:K.42, B:D.107, B:D.309 Water bridges: B:T.329 MES.18: 7 residues within 4Å: Chain A: K.42, Q.43, P.45 Chain C: Q.103, Y.104, D.107, D.309 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Water bridges: C:T.329, A:K.42 Salt bridges: C:D.107, C:D.309, A:K.42 MES.22: 7 residues within 4Å: Chain B: K.42, Q.43, P.45 Chain D: Q.103, Y.104, D.107, D.309 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B Salt bridges: D:D.107, D:D.309, B:K.42 Water bridges: B:K.42

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
A

D
A

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

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