SMTL ID : 6lbb.1

Crystal structure of barley exohydrolaseI W434A mutant in complex with 4I,4III,4V-S-trithiocellohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x GS1- SGC- BGC: beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1-thio-beta-D-glucopyranose

GS1-SGC-BGC.1: 19 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, A.438, Q.439, T.494, E.495, K.497 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:H.211, A:H.211, A:Q.439, A:K.497, A:G.61, A:Q.439, A:T.494, A:T.494 Water bridges: A:D.99, A:G.61

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

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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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:S.552 Water bridges: A:Q.379, A:Q.555, A:Q.555, A:Q.555 GOL.6: 5 residues within 4Å: Chain A: R.123, I.173, R.570, L.597, G.598 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.123, A:R.570 Water bridges: A:R.570 GOL.7: 4 residues within 4Å: Chain A: E.387, R.390, K.391, F.565 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.390, A:K.391 GOL.8: 4 residues within 4Å: Chain A: G.25, R.26, M.27, T.28 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.89 GOL.9: 3 residues within 4Å: Chain A: D.79, K.83, Y.367 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.83 GOL.10: 5 residues within 4Å: Chain A: L.407, P.411, S.482, Y.483, R.521 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.521 Water bridges: A:P.406, A:L.407, A:S.482

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

SO4.11: 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 SO4.12: 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

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

1PE.13: 5 residues within 4Å: Chain A: A.134, L.137, Q.375, K.378, H.381 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.134, A:H.381 1PE.14: 9 residues within 4Å: Chain A: E.490, H.491, P.492, Y.493, K.497, N.500, T.504, R.530 Ligands: ACT.18 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.490, A:E.490, A:N.500, A:R.530 Water bridges: A:H.491, A:H.491 1PE.15: 2 residues within 4Å: Chain A: K.309, V.340 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.309 1PE.16: 2 residues within 4Å: Chain A: K.281, K.283 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.283 Water bridges: A:K.277, A:D.278, A:K.281 1PE.17: 4 residues within 4Å: Chain A: E.17, M.196, K.283, R.355 No protein-ligand interaction detected (PLIP)

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

ACT.18: 2 residues within 4Å: Chain A: H.491 Ligands: 1PE.14 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.491 Salt bridges: A:H.491 ACT.19: 4 residues within 4Å: Chain A: L.594, F.595, R.596, Y.599 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.596 Water bridges: A:R.596 ACT.20: 2 residues within 4Å: Chain A: N.604, A.605 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.566, A:A.605 Water bridges: A:T.603 ACT.21: 2 residues within 4Å: Chain A: G.443, R.444 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.444

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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