SMTL ID : 4zod.1

Crystal Structure of beta-glucosidase from Listeria innocua in complex with glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

3 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.1: 14 residues within 4Å: Chain A: L.61, D.91, F.135, R.149, K.191, H.192, M.235, F.238, D.270, W.271, M.302, W.409, E.473 Ligands: GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.149, A:R.149, A:K.191, A:H.192, A:H.192, A:E.473 Water bridges: A:K.191 BGC.10: 14 residues within 4Å: Chain B: L.61, D.91, F.135, R.149, K.191, H.192, M.235, F.238, D.270, W.271, M.302, W.409, E.473 Ligands: GOL.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.149, B:R.149, B:K.191, B:H.192, B:H.192, B:E.473 BGC.11: 6 residues within 4Å: Chain A: H.690 Chain B: T.212, D.242, I.244, N.249, W.251 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.212, B:D.242, B:N.249 Water bridges: B:W.251 Salt bridges: A:H.690

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.648, T.650, A.651 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.648, A:T.650, H2O.3, H2O.4, H2O.4, H2O.7 MG.12: 3 residues within 4Å: Chain B: D.648, T.650, A.651 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.648, B:T.650, H2O.12, H2O.13, H2O.15, H2O.17

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: W.271, E.473 Chain B: R.572 Ligands: BGC.1 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.572, B:R.572, A:E.473 GOL.4: 8 residues within 4Å: Chain A: R.143, E.214, N.218, Y.564, N.566, L.568 Chain B: T.207, N.209 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.143, A:N.218, A:Y.564 Water bridges: A:R.143, A:N.218, A:Y.564, A:N.566, A:L.568 GOL.5: 4 residues within 4Å: Chain A: E.438, Y.439, T.440, K.467 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.439, A:T.440, A:T.440, A:K.467, A:K.467 GOL.8: 5 residues within 4Å: Chain A: R.572 Chain B: F.238, W.271, E.473 Ligands: BGC.10 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.572, A:R.572, B:E.473 GOL.13: 8 residues within 4Å: Chain A: T.207, N.209 Chain B: R.143, E.214, N.218, Y.564, N.566, L.568 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.143, B:Y.564, B:Y.564 Water bridges: B:E.214, A:N.209 GOL.14: 6 residues within 4Å: Chain B: Y.216, L.220, N.224, E.260, M.261, Y.688 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.260 GOL.15: 4 residues within 4Å: Chain B: E.438, Y.439, T.440, K.467 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.439, B:T.440, B:T.440, B:K.467

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 5 residues within 4Å: Chain A: W.470, L.477, R.481, L.482, P.483 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.482 PEG.9: 4 residues within 4Å: Chain A: T.212, N.249, W.251 Chain B: H.690 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.212, A:T.212, A:N.249 Water bridges: A:D.242, A:N.249

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 5 residues within 4Å: Chain A: S.211, T.212, D.242 Chain B: S.211, T.212 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.212, B:T.212, A:T.212, A:T.212 Water bridges: B:R.213, A:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakajima, M. et al., Functional and Structural Analysis of a beta-Glucosidase Involved in beta-1,2-Glucan Metabolism in Listeria innocua. Plos One (2016)

Release Date

2016-05-18

Peptides

Lin1840 protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lin1840 protein

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