SMTL ID : 4zob.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

5 x LGC: D-glucono-1,5-lactone(Non-covalent)

LGC.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.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.149, A:R.149, A:K.191, A:H.192, A:E.473 LGC.2: 6 residues within 4Å: Chain A: T.212, D.242, I.244, 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, A:N.249 Water bridges: A:W.251 LGC.8: 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.6 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.149, B:R.149, B:K.191, B:H.192, B:E.473 Water bridges: B:K.191 LGC.9: 7 residues within 4Å: Chain A: H.690 Chain B: T.212, D.242, I.244, N.249, W.251 Ligands: SO4.14 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.212, B:T.212, B:N.249 Water bridges: B:N.249, B:W.251 LGC.10: 7 residues within 4Å: Chain A: Y.583 Chain B: G.408, W.409, N.410, N.468, G.472, E.473 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.409, B:W.409, B:N.410, B:E.473, B:E.473

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: D.648, T.650, A.651 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.648, A:T.650, H2O.2, H2O.3, H2O.5 MG.11: 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.9, H2O.10, H2O.10, H2O.11

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: F.238, W.271, E.473 Chain B: R.572 Ligands: LGC.1 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.572, B:R.572, A:E.473 Water bridges: B:Y.583 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:E.438, A:Y.439, A:T.440, A:K.467, A:K.467 GOL.6: 6 residues within 4Å: Chain A: R.572, Y.583 Chain B: F.238, W.271, E.473 Ligands: LGC.8 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.12: 5 residues within 4Å: Chain A: D.589 Chain B: W.470, L.477, R.481, P.483 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.481 GOL.13: 6 residues within 4Å: Chain B: P.158, Q.217, N.218, P.221, E.659, K.661 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.217, B:Q.217, B:N.218, B:K.661, B:K.661 Water bridges: B:F.159, B:E.659

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

PEG.7: 9 residues within 4Å: Chain A: T.207, N.209, G.243 Chain B: R.143, R.213, E.214, N.218, Y.564, N.566 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:N.209, A:G.243, B:R.143, B:R.213, B:N.218, B:Y.564, B:N.566 Water bridges: B:R.213, B:N.566, B:L.568

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

SO4.14: 6 residues within 4Å: Chain A: S.211, T.212 Chain B: S.211, T.212, D.242 Ligands: LGC.9 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:T.212, B:T.212 Water bridges: A:R.213, B:R.213, B:R.213, B:D.242

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

Related Entries With Identical Sequence