SMTL ID : 6jg6.1

Crystal structure of barley exohydrolaseI W286A mutant in complex with methyl 6-thio-beta-gentiobioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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: 17 residues within 4Å: Chain A: E.40, L.58, G.60, G.61, D.99, F.148, R.162, K.210, H.211, M.254, Y.257, D.289, M.320, W.434, W.438, E.495 Ligands: GOL.10 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:E.40, A:G.61 Water bridges: A:K.210, A:E.495

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.2: 4 residues within 4Å: Chain A: E.224, N.225, N.226, S.259 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.226 Hydrogen bonds: A:K.264 Water bridges: A:N.225, A:N.225, A:N.225, A:T.298 NAG.3: 4 residues within 4Å: Chain A: D.499, N.500, N.502, T.504 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.499, A:N.502 Water bridges: A:N.500, A:L.501, A:T.504, A:T.504 NAG.4: 1 residues within 4Å: Chain A: N.604 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.604

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

1PE.5: 2 residues within 4Å: Chain A: R.171, R.172 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.171, A:R.171 Water bridges: A:Q.175, A:Q.175, A:Q.175 1PE.6: 6 residues within 4Å: Chain A: E.133, A.134, L.137, Q.375, K.378, H.381 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.378 Water bridges: A:R.130, A:A.134, A:Q.375, A:H.381 1PE.7: 6 residues within 4Å: Chain A: F.467, A.468, E.469, N.470, P.471, F.475 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.469, A:N.470 1PE.8: 5 residues within 4Å: Chain A: Q.175, S.176, T.178, N.244, K.248 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.244, A:K.248, A:K.248 Water bridges: A:S.176 1PE.9: 2 residues within 4Å: Chain A: K.281, K.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.283 Water bridges: A:K.277, A:D.278

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: E.224, Y.257, A.290, R.295 Ligands: U1Y-BGC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.224, A:E.291, A:R.295, A:R.295 GOL.11: 4 residues within 4Å: Chain A: R.123, I.173, L.597, G.598 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.123, A:R.123 GOL.12: 3 residues within 4Å: Chain A: R.390, K.391, F.565 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 Water bridges: A:R.130 GOL.13: 2 residues within 4Å: Chain A: K.456, A.457 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.456 GOL.14: 3 residues within 4Å: Chain A: T.28, A.30, F.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.28, A:T.28 GOL.15: 5 residues within 4Å: Chain A: Q.379, R.382, G.448, T.449, E.553 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.449, A:T.449, A:E.553 Water bridges: A:Q.379, A:R.382, A:Q.555, A:Q.555 GOL.17: 3 residues within 4Å: Chain A: P.342, M.343, S.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.343, A:S.344, A:S.344

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

SO4.16: 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

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

2020-08-19

Peptides

BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1