SMTL ID : 5z87.1

Structural of a novel b-glucosidase EmGH1 at 2.3 angstrom from Erythrobacter marinus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.1: 11 residues within 4Å: Chain A: Y.93, E.130, F.178, R.192, K.233, H.234, H.281, D.313, W.314, Y.452, E.541 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.192, A:R.192, A:K.233, A:H.234 DTT.16: 10 residues within 4Å: Chain B: Y.93, E.130, F.178, R.192, K.233, H.234, H.281, D.313, Y.452, E.541 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.192, B:R.192, B:K.233, B:H.234

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.538, R.552, R.583, L.585 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: D.713, I.715 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.713, A:I.715, H2O.1, H2O.3, H2O.3, H2O.4 MG.4: 2 residues within 4Å: Chain A: D.292, H.294 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.292 MG.18: 5 residues within 4Å: Chain B: G.534, T.538, R.552, R.583, L.585 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain B: D.713, I.715 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.713, B:I.715, H2O.21, H2O.24, H2O.24, H2O.25

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 6 residues within 4Å: Chain A: Q.240, P.637, Y.639 Chain B: I.242, H.251 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.639, A:Y.639 Water bridges: A:Q.240 GOL.6: 5 residues within 4Å: Chain A: D.57, Y.84, H.87, P.356, R.360 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.87, A:R.360, A:R.360 Water bridges: A:Q.357 GOL.15: 6 residues within 4Å: Chain A: I.242, H.251 Chain B: Q.240, P.637, Y.639 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.639 Water bridges: B:E.256 GOL.20: 5 residues within 4Å: Chain B: D.57, Y.84, H.87, P.356, R.360 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.57, B:H.87, B:R.360, B:R.360 Water bridges: B:D.57, B:D.57, B:Q.357 GOL.21: 8 residues within 4Å: Chain B: I.269, G.273, S.274, I.275, F.306, E.307, G.308, K.382 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.273, B:E.307, B:G.308, B:K.382

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: V.619, N.620, A.702, G.703, L.732 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.620 Water bridges: A:Q.704, A:Q.704 EDO.8: 5 residues within 4Å: Chain A: Q.677, E.679, R.690, S.692, Q.742 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.742 Water bridges: A:S.692, A:S.692 EDO.9: 6 residues within 4Å: Chain A: R.266, D.303, R.753, D.756, G.757, K.758 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.266, A:R.753, A:D.756 EDO.10: 5 residues within 4Å: Chain A: D.553, D.554 Chain B: F.653, S.654 Ligands: PEG.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.654 Water bridges: B:S.654 EDO.11: 1 residues within 4Å: Chain A: S.117 No protein-ligand interaction detected (PLIP) EDO.22: 5 residues within 4Å: Chain B: V.619, N.620, A.702, G.703, L.732 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.620 Water bridges: B:Q.704 EDO.23: 4 residues within 4Å: Chain B: L.429, Q.430, V.527, T.574 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.430, B:Q.430

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

PEG.12: 7 residues within 4Å: Chain A: P.201, H.202, T.205, N.259, P.263, R.726 Ligands: PEG.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.202, A:R.726 Water bridges: A:R.726, A:D.749 PEG.13: 9 residues within 4Å: Chain A: P.201, N.259, V.260, Y.641, P.721, E.724, R.726 Ligands: PEG.12, PEG.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.726, A:R.726 Water bridges: A:M.725, A:M.725 PEG.14: 11 residues within 4Å: Chain A: V.255, N.259, K.643, A.719, R.720, P.721, E.724, Y.752 Chain B: D.285, G.286 Ligands: PEG.13 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.285, A:K.643, A:R.720, A:E.724 PEG.24: 6 residues within 4Å: Chain A: D.553, D.554, V.633 Chain B: L.588, N.632 Ligands: EDO.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.632, A:D.553 Water bridges: B:S.654, A:D.554 PEG.25: 9 residues within 4Å: Chain B: I.252, G.253, P.254, M.257, I.284, V.287, D.292, H.294, L.295 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:R.718 Hydrogen bonds: B:I.252, B:I.284 PEG.26: 9 residues within 4Å: Chain B: V.255, N.259, K.643, A.719, R.720, P.721, E.724, R.726, Y.752 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.643, B:A.719, B:R.720, B:R.726 Water bridges: B:R.726, B:G.751

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.17: 6 residues within 4Å: Chain B: V.116, S.117, S.119, R.120, F.121, G.122 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.116 Hydrogen bonds: B:V.116, B:R.120

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, L. et al., Structural and biochemical analysis of a novel b-glucosidase EmGH1 from Erythrobacter marinus. To Be Published

Release Date

2019-02-06

Peptides

EmGH1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

EmGH1