SMTL ID : 6jga.1

Crystal structure of barley exohydrolaseI W286F in complex with 4'-nitrophenyl thiolaminaribioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

monomer

Ligands

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

6BV.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, 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:D.99, A:R.162, A:R.162, A:K.210, A:R.295, A:R.295, A:E.495 Water bridges: A:K.210, A:E.495, A:E.495

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

NAG.2: 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 Water bridges: A:N.500, A:L.501, A:T.504 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: 5 residues within 4Å: Chain A: E.224, N.225, N.226, S.259, K.264 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.226 Hydrogen bonds: A:K.264 Water bridges: A:N.225

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

1PE.5: 1 residues within 4Å: Chain A: K.416 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.416 1PE.6: 8 residues within 4Å: Chain A: H.491, P.492, Y.493, K.497, G.498, N.500, R.530 Ligands: SO4.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.500, A:R.530 Water bridges: A:H.491 1PE.7: 5 residues within 4Å: Chain A: 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 1PE.8: 4 residues within 4Å: Chain A: E.387, R.390, K.391, F.565 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.390, A:R.390, A:K.391 Water bridges: A:D.124 1PE.9: 3 residues within 4Å: Chain A: P.15, V.16, E.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.16, A:E.17 Water bridges: A:E.17, A:E.17 1PE.10: 4 residues within 4Å: Chain A: L.594, F.595, R.596, Y.599 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.596, A:R.596 Water bridges: A:Y.599, A:Y.599, A:Y.599

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 1 residues within 4Å: Chain A: K.456 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.456 GOL.12: 3 residues within 4Å: Chain A: P.411, K.412, K.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.412, A:K.413 GOL.13: 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 Water bridges: A:Q.379, A:Q.379, A:Q.379, A:G.448, A:T.449, A:E.553, A:Q.555

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

SO4.14: 3 residues within 4Å: Chain A: P.342, M.343, S.344 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.343, A:S.344 Water bridges: A:S.344 SO4.15: 3 residues within 4Å: Chain A: T.298, P.299, A.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.298, A:A.300 SO4.16: 2 residues within 4Å: Chain A: H.491 Ligands: 1PE.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.491 Salt bridges: A:H.491 SO4.17: 6 residues within 4Å: Chain A: Q.175, S.176, T.178, E.179, N.244, K.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.179, A:N.244 Salt bridges: A:K.248

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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