SMTL ID : 6jg2.1

Crystal structure of barley exohydrolaseI wildtype in complex with 4'-nitrophenyl thiolaminaribioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

NAG.1: 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 Hydrogen bonds: A:K.264 NAG.2: 1 residues within 4Å: Chain A: N.604 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.604

1 x BV6: (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-nitrophenoxy)-3,5-bis(oxidanyl)oxan-4-yl]sulfanyl-oxane-3,4,5-triol(Non-covalent)

BV6.3: 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, W.438, E.495 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.61, A:G.61, A:R.162, A:R.162, A:K.210, A:H.211, A:E.495 Water bridges: A:S.59, A:D.99, A:K.210, A:N.223, A:D.289

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

1PE.4: 6 residues within 4Å: Chain A: R.172, Q.175, S.176, N.244, K.248 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.175, A:S.176, A:N.244, A:K.248 1PE.5: 7 residues within 4Å: Chain A: Y.126, E.133, A.134, E.380, H.381, L.384 Ligands: 1PE.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.126, A:E.380, A:H.381 1PE.6: 3 residues within 4Å: Chain A: D.79, K.83, Y.367 No protein-ligand interaction detected (PLIP) 1PE.7: 4 residues within 4Å: Chain A: E.133, L.137, H.381 Ligands: 1PE.5 No protein-ligand interaction detected (PLIP)

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

SO4.8: 5 residues within 4Å: Chain A: P.593, L.594, F.595, R.596, Y.599 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.596 Salt bridges: A:R.596 SO4.9: 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 SO4.10: 6 residues within 4Å: Chain A: R.123, P.125, I.173, S.176, M.177 Ligands: 1PE.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.176 SO4.11: 4 residues within 4Å: Chain A: A.468, E.469, N.470, P.471 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.470 Water bridges: A:E.469, A:E.469

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 2 residues within 4Å: Chain A: D.303, Y.306 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.303, A:D.303

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

Barley exohydrolase I: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Barley exohydrolase I

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