SMTL ID : 6jgn.1

Crystal structure of barley exohydrolaseI W434H in complex with 4'-nitrophenyl thiolaminaribioside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

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

LAM.1: 14 residues within 4Å: Chain A: D.99, F.148, R.162, K.210, H.211, M.254, Y.257, D.289, W.290, R.295, M.320, W.434 Ligands: GOL.3, 1PE.15 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.162, A:R.162, A:K.210, A:H.211, A:R.295 Water bridges: A:G.61, A:G.61, A:K.210, A:Y.257, A:R.295, A:R.295

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: G.25, R.26, M.27, T.28 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.26, A:R.89 GOL.3: 11 residues within 4Å: Chain A: W.160, R.162, H.211, D.215, E.224, I.255, S.256, Y.257, D.289, E.495 Ligands: LAM.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.162, A:S.256, A:Y.257, A:D.289, A:D.289, A:E.495 GOL.4: 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:I.341 GOL.5: 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.6: 7 residues within 4Å: Chain A: Q.379, R.382, V.447, G.448, T.449, S.552, E.553 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.379, A:T.449, A:E.553 Water bridges: A:Q.555, A:Q.555 GOL.7: 5 residues within 4Å: Chain A: D.170, R.171, R.172, V.586 Ligands: ACT.28 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.170, A:R.171 Water bridges: A:R.156, A:E.169 GOL.8: 6 residues within 4Å: Chain A: R.156, T.218, P.583, N.585, D.588 Ligands: 1PE.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.156, A:N.585 Water bridges: A:T.218, A:T.218 GOL.9: 3 residues within 4Å: Chain A: T.28, A.30, F.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.28 Water bridges: A:T.28, A:L.29

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

1PE.10: 8 residues within 4Å: Chain A: Y.126, R.130, E.133, A.134, L.137, Q.375, K.378, H.381 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.126, A:Y.126 Water bridges: A:H.381 1PE.11: 6 residues within 4Å: Chain A: E.17, D.347, D.348, T.351, R.355 Ligands: ACT.25 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.355 Water bridges: A:D.348, A:R.352, A:R.355 1PE.12: 6 residues within 4Å: Chain A: R.172, Q.175, S.176, T.178, N.244, K.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.244, A:K.248, A:K.248 1PE.13: 6 residues within 4Å: Chain A: E.232, G.587, D.588, A.589 Ligands: GOL.8, 1PE.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.236 1PE.14: 5 residues within 4Å: Chain A: K.397, G.399, K.400, T.401, S.402 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.397 1PE.15: 8 residues within 4Å: Chain A: R.162, W.434, H.438, T.494, E.495, T.496, K.497 Ligands: LAM.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.162, A:T.494, A:T.496, A:K.497 Water bridges: A:R.162, A:E.165 1PE.16: 4 residues within 4Å: Chain A: E.387, R.390, K.391, F.565 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.390, A:R.390 1PE.17: 4 residues within 4Å: Chain A: G.201, K.202, G.361, N.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.202, A:G.361, A:N.365 1PE.18: 5 residues within 4Å: Chain A: A.468, P.471, D.472, F.475 Ligands: ACT.29 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.472, A:D.472 1PE.19: 4 residues within 4Å: Chain A: L.594, F.595, R.596, Y.599 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.596 1PE.20: 6 residues within 4Å: Chain A: N.52, Y.325, Q.326, I.329, S.330 Ligands: ACT.34 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.52, A:N.52 1PE.21: 2 residues within 4Å: Chain A: E.232 Ligands: 1PE.13 No protein-ligand interaction detected (PLIP) 1PE.22: 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.23: 2 residues within 4Å: Chain A: N.223, T.496 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.223, A:N.223

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

ACT.24: 4 residues within 4Å: Chain A: K.67, I.436, D.441, T.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.441 Water bridges: A:K.67, A:K.67 Salt bridges: A:K.67 ACT.25: 5 residues within 4Å: Chain A: E.17, M.196, K.283, R.355 Ligands: 1PE.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.283 Salt bridges: A:R.355 ACT.26: 3 residues within 4Å: Chain A: E.291, N.323, K.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.323 Water bridges: A:K.324 Salt bridges: A:K.324 ACT.27: 4 residues within 4Å: Chain A: E.224, N.225, K.264, R.295 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.225 Hydrogen bonds: A:E.224 Salt bridges: A:K.264, A:R.295 ACT.28: 3 residues within 4Å: Chain A: R.171, R.172 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.171 ACT.29: 4 residues within 4Å: Chain A: E.469, N.470, P.471 Ligands: 1PE.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.469, A:N.470, A:N.470 ACT.30: 3 residues within 4Å: Chain A: T.298, P.299, A.300 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.298, A:P.299 Hydrogen bonds: A:A.300 ACT.31: 2 residues within 4Å: Chain A: T.28, L.29 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.29 Hydrogen bonds: A:L.29 Water bridges: A:A.30 ACT.32: 2 residues within 4Å: Chain A: D.79, Y.367 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.367 Hydrogen bonds: A:D.79 ACT.33: 2 residues within 4Å: Chain A: D.303, Y.306 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.306 ACT.34: 3 residues within 4Å: Chain A: D.47, V.48 Ligands: 1PE.20 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.47 ACT.35: 3 residues within 4Å: Chain A: D.270, G.274, Y.275 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.270

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

SO4.36: 6 residues within 4Å: Chain A: R.123, D.124, P.125, I.173, S.176, M.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.176 SO4.37: 3 residues within 4Å: Chain A: S.422, Y.429, E.469 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.469 Water bridges: A:N.426

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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