SMTL ID : 2z8f.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-tetraose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

4 x BGC- GAL- NAG- GAL: beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose

BGC-GAL-NAG-GAL.1: 21 residues within 4Å: Chain A: R.23, L.24, P.25, A.58, S.59, Q.79, D.128, D.176, E.177, N.180, W.231, W.252, L.256, G.288, G.289, S.290, L.323, S.368, A.371, A.372, N.375 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.59, A:S.368, A:Q.79, A:G.289, A:S.290, A:S.290, A:R.23, A:R.23 Water bridges: A:K.57, A:S.59, A:N.375, A:R.23, A:R.23, A:R.23, A:S.290, A:A.58, A:Q.79, A:E.177, A:N.180 BGC-GAL-NAG-GAL.7: 21 residues within 4Å: Chain B: R.23, L.24, P.25, A.58, S.59, Q.79, D.128, D.176, E.177, N.180, W.231, W.252, L.256, G.288, G.289, S.290, L.323, S.368, A.371, A.372, N.375 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.59, B:S.368, B:Q.79, B:G.289, B:S.290, B:S.290, B:R.23, B:R.23 Water bridges: B:K.57, B:S.59, B:N.375, B:R.23, B:R.23, B:R.23, B:S.290, B:A.58, B:Q.79, B:E.177, B:N.180 BGC-GAL-NAG-GAL.13: 20 residues within 4Å: Chain C: R.23, L.24, P.25, A.58, S.59, Q.79, D.128, D.176, E.177, N.180, W.231, W.252, G.288, G.289, S.290, L.323, S.368, A.371, A.372, N.375 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.59, C:S.368, C:N.375, C:Q.79, C:G.289, C:S.290, C:S.290, C:R.23, C:R.23 Water bridges: C:E.376, C:E.376, C:R.23, C:R.23, C:R.23, C:S.290, C:A.58, C:Q.79, C:E.177, C:N.180 BGC-GAL-NAG-GAL.19: 20 residues within 4Å: Chain D: R.23, L.24, P.25, A.58, S.59, Q.79, D.128, D.176, E.177, N.180, W.231, W.252, G.288, G.289, S.290, L.323, S.368, A.371, A.372, N.375 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:S.59, D:S.368, D:N.375, D:Q.79, D:G.289, D:S.290, D:S.290, D:R.23, D:R.23 Water bridges: D:R.23, D:R.23, D:R.23, D:S.290, D:A.58, D:Q.79, D:E.177, D:N.180

10 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.12, H.300, E.303 Chain C: D.11 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Metal complexes: A:D.12, A:H.300, A:E.303, C:D.11, C:D.11 ZN.3: 3 residues within 4Å: Chain A: H.44, D.46 Chain C: E.306 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: A:H.44, A:D.46, C:E.306, C:E.306, H2O.4 ZN.8: 4 residues within 4Å: Chain B: D.12, H.300, E.303 Chain D: D.11 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain B Metal complexes: D:D.11, D:D.11, B:D.12, B:H.300, B:E.303 ZN.9: 3 residues within 4Å: Chain B: H.44, D.46 Chain D: E.306 5 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: D:E.306, D:E.306, B:H.44, B:D.46, H2O.23 ZN.14: 4 residues within 4Å: Chain A: D.11 Chain C: D.12, H.300, E.303 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Metal complexes: C:D.12, C:H.300, C:E.303, A:D.11 ZN.15: 4 residues within 4Å: Chain A: E.306 Chain C: Q.43, 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.9 ZN.16: 7 residues within 4Å: Chain C: D.331, E.333 Chain D: D.331, E.333 Ligands: NA.17, ZN.22, NA.23 5 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: D:E.333, C:E.333, H2O.46, H2O.52, H2O.70 ZN.20: 4 residues within 4Å: Chain B: D.11 Chain D: D.12, H.300, E.303 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Metal complexes: D:D.12, D:H.300, D:E.303, B:D.11 ZN.21: 4 residues within 4Å: Chain B: E.306 Chain D: Q.43, H.44, D.46 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: B:E.306, B:E.306, D:H.44, D:D.46, H2O.28 ZN.22: 7 residues within 4Å: Chain C: D.331, E.333 Chain D: D.331, E.333 Ligands: ZN.16, NA.17, NA.23 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: C:E.333, D:E.333, H2O.52, H2O.64, H2O.70

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

NA.4: 1 residues within 4Å: Chain A: D.198 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.198 NA.5: 1 residues within 4Å: Chain A: D.394 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.394 NA.10: 1 residues within 4Å: Chain B: D.198 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.198 NA.11: 1 residues within 4Å: Chain B: D.394 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.394 NA.17: 5 residues within 4Å: Chain C: D.331, E.333 Chain D: D.331 Ligands: ZN.16, ZN.22 2 PLIP interactions: 2 interactions with chain C Water bridges: C:D.331, C:D.331 NA.23: 5 residues within 4Å: Chain C: D.331 Chain D: D.331, E.333 Ligands: ZN.16, ZN.22 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.331 Water bridges: D:D.331

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

MES.6: 8 residues within 4Å: Chain A: Q.103, Y.104, D.107, D.309, T.329 Chain C: K.42, Q.43, P.45 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Salt bridges: C:K.42, A:D.107, A:D.309 MES.12: 8 residues within 4Å: Chain B: Q.103, Y.104, D.107, D.309, T.329 Chain D: K.42, Q.43, P.45 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D Salt bridges: B:D.107, B:D.309, D:K.42 MES.18: 8 residues within 4Å: Chain A: K.42, Q.43, P.45 Chain C: Q.103, Y.104, D.107, D.309, T.329 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Salt bridges: C:D.107, C:D.309 Hydrogen bonds: A:Q.43 MES.24: 8 residues within 4Å: Chain B: K.42, Q.43, P.45 Chain D: Q.103, Y.104, D.107, D.309, T.329 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Salt bridges: D:D.107, D:D.309 Hydrogen bonds: B:Q.43

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
A

B
A

C
B

D
B

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

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