SMTL ID : 6jg1.1

Crystal structure of barley exohydrolaseI wildtype in complex with 4I,4III,4V-S-trithiocellohexaose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x GS1- SGC- BGC: beta-D-glucopyranose-(1-4)-4-thio-beta-D-glucopyranose-(1-4)-1-thio-beta-D-glucopyranose

GS1-SGC-BGC.1: 18 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, E.291, R.295, M.320, W.434, W.438, E.495 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:G.61, A:Y.257, A:R.295, A:R.295 Water bridges: A:D.99

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

NAG.2: 4 residues within 4Å: Chain A: D.499, N.500, N.502, T.504 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.499 Water bridges: A:L.501, A:T.504, A:T.504 NAG.3: 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 NAG.4: 2 residues within 4Å: Chain A: T.602, N.604 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.604 Water bridges: A:N.604

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

1PE.5: 2 residues within 4Å: Chain A: T.122, R.123 No protein-ligand interaction detected (PLIP) 1PE.6: 5 residues within 4Å: Chain A: A.134, L.137, Q.375, K.378, H.381 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.134 1PE.7: 2 residues within 4Å: Chain A: T.401, S.402 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.402 1PE.8: 3 residues within 4Å: Chain A: K.283, R.355 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.348, A:R.355 1PE.9: 3 residues within 4Å: Chain A: R.26, M.27, T.28 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.29, A:L.29 1PE.10: 4 residues within 4Å: Chain A: T.297, T.298, S.302, D.303 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.303, A:D.303 Water bridges: A:T.298 1PE.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 1PE.12: 5 residues within 4Å: Chain A: K.416, F.475, S.478, G.479, G.480 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.416 Water bridges: A:K.416, A:K.416

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.13: 5 residues within 4Å: Chain A: R.123, I.173, R.570, L.597, G.598 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.123, A:R.570, A:R.570 Water bridges: A:D.170 GOL.14: 2 residues within 4Å: Chain A: R.171, R.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.171, A:R.171 Water bridges: A:Q.175, A:Q.175 GOL.15: 3 residues within 4Å: Chain A: K.281, K.283 Ligands: 1PE.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.283

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

SO4.16: 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 SO4.17: 2 residues within 4Å: Chain A: R.390, K.391 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.390, A:R.390 Salt bridges: A:R.390, A:K.391 SO4.18: 1 residues within 4Å: Chain A: H.491 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.491

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

Related Entries With Identical Sequence