SMTL ID : 6l1j.1

Crystal structure of barley exohydrolaseI W434A mutant in complex with 4'-nitrophenyl thiolaminaritrioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: E.224, N.225, N.226, S.259 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.226 Hydrogen bonds: A:K.264 Water bridges: A:N.225, A:N.225 NAG.2: 1 residues within 4Å: Chain A: N.604 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.604 NAG.3: 4 residues within 4Å: Chain A: D.499, N.500, N.502, T.504 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.499, A:N.502 Water bridges: A:L.501, A:L.503, A:T.504

1 x LAM: 4'-NITROPHENYL-S-(BETA-D-GLUCOPYRANOSYL)-(1-3)-(3-THIO-BETA-D-GLUCOPYRANOSYL)-(1-3)-BETA-D-GLUCOPYRANOSIDE(Non-covalent)

LAM.4: 16 residues within 4Å: Chain A: L.58, 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, E.495 Ligands: GOL.8 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:K.210, A:H.211, A:E.224, A:R.295, A:R.295 Water bridges: A:G.61, A:G.61, A:K.210, A:N.223, A:D.289 Salt bridges: A:R.295

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

ACT.5: 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.6: 3 residues within 4Å: Chain A: T.298, P.299, A.300 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.299 Hydrogen bonds: A:A.300

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: G.25, R.26, M.27, T.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.25 Water bridges: A:R.26, A:R.89 GOL.8: 10 residues within 4Å: Chain A: R.162, H.211, D.215, N.223, E.224, S.256, Y.257, S.258, D.289 Ligands: LAM.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.162, A:N.223, A:E.224, A:Y.257, A:S.258, A:D.289 GOL.9: 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:S.552 Water bridges: A:Q.379, A:E.553, A:E.553, A:Q.555, A:Q.555 GOL.10: 8 residues within 4Å: Chain A: E.490, H.491, Y.493, K.497, G.498, N.500, P.506, R.530 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.491, A:G.498, A:N.500, A:R.530 Water bridges: A:E.490, A:H.491, A:H.491

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

SO4.11: 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.12: 2 residues within 4Å: Chain A: K.281, K.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.283 1PE.13: 3 residues within 4Å: Chain A: E.17, M.196, K.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.283 1PE.14: 3 residues within 4Å: Chain A: P.15, V.16, E.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.16, A:E.17 Water bridges: A:E.17 1PE.15: 4 residues within 4Å: Chain A: A.134, L.137, Q.375, H.381 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.375 Water bridges: A:A.134, A:H.381 1PE.16: 4 residues within 4Å: Chain A: E.291, D.294, R.295, A.300 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.295

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 GLUCOHYDROLASE ISOENZYME EXO1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BETA-D-GLUCAN GLUCOHYDROLASE ISOENZYME EXO1

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