SMTL ID : 6jgl.1

Crystal structure of barley exohydrolaseI W434H mutant in complex with methyl 2-thio-beta-sophoroside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

1 x U2A- BGC: beta-D-glucopyranose-(1-2)-methyl 2-thio-beta-D-glucopyranoside(Non-covalent)

U2A-BGC.1: 19 residues within 4Å: Chain A: L.58, G.60, G.61, D.99, F.148, R.162, K.210, H.211, E.224, M.254, Y.257, D.289, W.290, R.295, M.320, W.434, H.438, E.495 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:K.210, A:H.211, A:H.211, A:R.295, A:R.295, A:E.495 Water bridges: A:K.210, A:D.289 Salt bridges: A:H.438

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

NAG.2: 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.3: 5 residues within 4Å: Chain A: E.224, N.225, N.226, S.259, K.264 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.4: 3 residues within 4Å: Chain A: D.499, N.500, N.502 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.499, A:N.502 Water bridges: A:L.501, A:L.501

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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.123, A:R.570 GOL.6: 8 residues within 4Å: Chain A: G.60, G.61, W.290, W.434, H.438, E.495 Ligands: U2A-BGC.1, U2A-BGC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.61, A:D.99 GOL.7: 6 residues within 4Å: Chain A: Y.429, Q.439, G.440, D.441, H.491, P.492 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.440 Water bridges: A:D.441, A:T.442

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

SO4.8: 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 SO4.9: 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 SO4.10: 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 Water bridges: A:R.596 Salt bridges: A:R.596 SO4.11: 2 residues within 4Å: Chain A: G.443, R.444 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.444

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

1PE.12: 3 residues within 4Å: Chain A: K.72, E.73, D.76 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.76 1PE.13: 3 residues within 4Å: Chain A: V.533, Q.535, K.577 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.535

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

ACT.14: 2 residues within 4Å: Chain A: P.15, V.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.15 Hydrogen bonds: A:V.16 ACT.15: 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 ACT.16: 2 residues within 4Å: Chain A: N.604, A.605 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.566, A:A.605 ACT.17: 3 residues within 4Å: Chain A: E.469, N.470, P.471 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.469 Hydrogen bonds: A:E.469, A:N.470, A:N.470 ACT.18: 2 residues within 4Å: Chain A: R.390, F.565 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.391, A:K.391 Salt bridges: A:R.390, A:K.391

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

Related Entries With Identical Sequence