SMTL ID : 6jgs.1

Crystal structure of barley exohydrolaseI W434Y mutant in complex with 4I,4III,4V-S-trithiocellohexaose.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

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

SGC-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, W.290, R.295, M.320, W.434, Y.438, E.495 4 PLIP interactions: 4 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, A:Y.257, A:R.295, A:R.295 Water bridges: A:K.210, A:D.289

2 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 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.226 Water bridges: 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

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: A.200, G.201, K.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.202 GOL.5: 3 residues within 4Å: Chain A: R.390, K.391, F.565 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 GOL.6: 5 residues within 4Å: Chain A: R.123, I.173, R.570, L.597, G.598 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.123, A:R.570

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

ACT.7: 3 residues within 4Å: Chain A: G.566, N.604, A.605 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.566, A:A.605 ACT.8: 4 residues within 4Å: Chain A: A.267, N.268, Q.269, D.270 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.269, A:D.270, A:D.270 Water bridges: A:N.268, A:D.270 ACT.9: 5 residues within 4Å: Chain A: R.382, V.447, G.448, T.449, E.553 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.449, A:T.449 Water bridges: A:Q.555 Salt bridges: A:R.382 ACT.10: 2 residues within 4Å: Chain A: R.171, R.172 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.171, A:Q.175, A:Q.175 Salt bridges: A:R.171 ACT.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.12: 2 residues within 4Å: Chain A: K.309, V.340 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.335 Salt bridges: A:K.309

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

1PE.13: 7 residues within 4Å: Chain A: E.133, P.182, G.183, G.186, D.187, A.200, K.204 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.133, A:D.187, A:K.204 1PE.14: 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:Y.599 1PE.15: 3 residues within 4Å: Chain A: P.415, G.480, F.481 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.415 1PE.16: 1 residues within 4Å: Chain A: K.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.283 1PE.17: 4 residues within 4Å: Chain A: R.66, T.70, K.72, E.73 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.66, A:T.70, A:E.73 Water bridges: A:K.72 1PE.18: 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

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

SO4.19: 3 residues within 4Å: Chain A: T.298, P.299, A.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.300 Water bridges: A:T.298 SO4.20: 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

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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