SMTL ID : 6lbv.1

Crystal structure of barley exohydrolaseI W434F mutant in complex with methyl 6-thio-beta-gentiobioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

monomer

Ligands

1 x U1Y- BGC: beta-D-glucopyranose-(1-6)-methyl 6-thio-beta-D-glucopyranoside(Non-covalent)

U1Y-BGC.1: 16 residues within 4Å: Chain A: L.58, G.60, G.61, D.99, F.148, R.162, K.210, H.211, M.254, Y.257, D.289, W.290, M.320, W.434, F.438 Ligands: GOL.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.61, A:R.162, A:R.162, A:K.210, A:H.211, A:H.211, A:G.61 Water bridges: A:K.210, A:R.295

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: W.160, R.162, H.211, D.215, N.223, I.255, S.256, Y.257, S.258, D.289, E.495 Ligands: U1Y-BGC.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.162, A:N.223, A:Y.257, A:S.258, A:D.289, A:D.289, A:E.495 Water bridges: A:W.160, A:D.215 GOL.3: 4 residues within 4Å: Chain A: G.25, R.26, M.27, T.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.25 Water bridges: A:R.89, A:R.89 GOL.4: 2 residues within 4Å: Chain A: R.390, K.391 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 Water bridges: A:D.124 GOL.5: 5 residues within 4Å: Chain A: F.467, A.468, E.469, N.470, P.471 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.469, A:N.470, A:N.470 GOL.6: 5 residues within 4Å: Chain A: L.407, P.411, S.482, Y.483, R.521 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.482, A:R.521 GOL.7: 5 residues within 4Å: Chain A: Q.379, R.382, G.448, T.449, E.553 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.449, A:S.552 Water bridges: A:Q.379, A:Q.379, A:Q.555, A:Q.555

3 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.8: 3 residues within 4Å: Chain A: P.15, V.16, E.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.16, A:E.17 Water bridges: A:E.17, A:E.17 1PE.9: 8 residues within 4Å: Chain A: E.490, H.491, Y.493, K.497, G.498, N.500, P.506, R.530 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.490, A:H.491, A:P.506 Hydrogen bonds: A:G.498, A:N.500, A:R.530 Water bridges: A:K.497 1PE.10: 8 residues within 4Å: Chain A: S.422, H.423, Y.429, E.469, H.491, P.506, E.507, P.508 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.422, A:P.508 Water bridges: A:E.469, A:E.469, A:E.469

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

SO4.11: 3 residues within 4Å: Chain A: A.200, G.201, K.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.202 Water bridges: A:A.200, A:N.203 SO4.12: 3 residues within 4Å: Chain A: T.298, P.299, A.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.300 SO4.13: 3 residues within 4Å: Chain A: P.342, M.343, S.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.343, A:S.344

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.14: 3 residues within 4Å: Chain A: L.594, F.595, R.596 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.596 Salt bridges: A:R.596

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luang, S. et al., The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Nat Commun (2022)

Release Date

2020-09-30

Peptides

Beta-D-glucan exohydrolase isoenzyme ExoI: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-D-glucan exohydrolase isoenzyme ExoI

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