SMTL ID : 6jgb.1

Crystal structure of barley exohydrolaseI W286F mutant in complex with methyl 6-thio-beta-gentiobioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 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: L.58, G.60, G.61, D.99, F.148, R.162, K.210, H.211, M.254, Y.257, D.289, F.290, M.320, W.434, W.438, E.495 Ligands: 1PE.11 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

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

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: G.25, R.26, M.27, T.28 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.26, A:R.89 GOL.6: 3 residues within 4Å: Chain A: A.200, G.201, K.202 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.202, A:K.202 GOL.7: 5 residues within 4Å: Chain A: Q.379, R.382, G.448, T.449, E.553 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:T.449, A:T.449, A:S.552 Water bridges: A:Q.379, A:R.382, A:Q.555, A:Q.555, A:Q.555 GOL.8: 5 residues within 4Å: Chain A: P.593, L.594, F.595, R.596, Y.599 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.596, A:R.596 Water bridges: A:L.594 GOL.9: 2 residues within 4Å: Chain A: R.386, Q.555 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.386, A:R.386 Water bridges: A:Q.555, A:Q.555

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

SO4.10: 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

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

1PE.11: 9 residues within 4Å: Chain A: N.223, E.224, Y.257, F.290, R.295, W.438, E.495, T.496 Ligands: U1Y-BGC.1 Ligand excluded by PLIP 1PE.12: 9 residues within 4Å: Chain A: H.491, P.492, Y.493, K.497, G.498, N.500, R.530 Ligands: 1PE.25, ACT.28 Ligand excluded by PLIP 1PE.13: 6 residues within 4Å: Chain A: F.467, A.468, E.469, N.470, P.471, F.475 Ligand excluded by PLIP 1PE.14: 2 residues within 4Å: Chain A: G.68, Y.108 Ligand excluded by PLIP 1PE.15: 5 residues within 4Å: Chain A: A.134, L.137, Q.375, K.378, H.381 Ligand excluded by PLIP 1PE.16: 5 residues within 4Å: Chain A: Q.175, S.176, T.178, N.244, K.248 Ligand excluded by PLIP 1PE.17: 5 residues within 4Å: Chain A: T.13, K.14, P.15, V.16, E.17 Ligand excluded by PLIP 1PE.18: 2 residues within 4Å: Chain A: K.281, K.283 Ligand excluded by PLIP 1PE.19: 5 residues within 4Å: Chain A: A.267, N.268, Q.269, D.270 Ligands: 1PE.26 Ligand excluded by PLIP 1PE.20: 6 residues within 4Å: Chain A: K.202, N.365, Y.367, A.368, D.369 Ligands: ACT.30 Ligand excluded by PLIP 1PE.21: 4 residues within 4Å: Chain A: E.380, D.383, L.384, E.387 Ligand excluded by PLIP 1PE.22: 4 residues within 4Å: Chain A: D.425, N.426, G.443, R.444 Ligand excluded by PLIP 1PE.23: 3 residues within 4Å: Chain A: K.309, V.340 Ligands: 1PE.24 Ligand excluded by PLIP 1PE.24: 3 residues within 4Å: Chain A: Y.306, K.309 Ligands: 1PE.23 Ligand excluded by PLIP 1PE.25: 6 residues within 4Å: Chain A: Q.439, G.440, H.491, P.492 Ligands: 1PE.12, ACT.28 Ligand excluded by PLIP 1PE.26: 4 residues within 4Å: Chain A: Q.269, D.270, G.274 Ligands: 1PE.19 Ligand excluded by PLIP

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

ACT.27: 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 ACT.28: 3 residues within 4Å: Chain A: H.491 Ligands: 1PE.12, 1PE.25 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.491 ACT.29: 2 residues within 4Å: Chain A: E.17, M.196 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.283, A:K.283 Salt bridges: A:R.355 ACT.30: 2 residues within 4Å: Chain A: K.83 Ligands: 1PE.20 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.83 ACT.31: 2 residues within 4Å: Chain A: R.171 Ligands: ACT.32 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.175 Salt bridges: A:R.171 ACT.32: 4 residues within 4Å: Chain A: R.171, R.172, N.236 Ligands: ACT.31 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.236 Salt bridges: A:R.171, A:R.172 ACT.33: 2 residues within 4Å: Chain A: D.303, Y.306 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.303 ACT.34: 3 residues within 4Å: Chain A: Y.429, E.469, H.491 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.491

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

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