SMTL ID : 5cpt.1

Disproportionating enzyme 1 from Arabidopsis - beta cyclodextrin soak

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x BGC- GLC: alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose(Post Translational Modification)

BGC-GLC.1: 12 residues within 4Å: Chain A: S.122, Y.124, A.125, R.359, D.361, H.460, D.461, N.525, P.527, A.528, W.534 Ligands: EDO.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.359, A:H.460, A:H.460, A:N.525, A:S.122, A:D.461, A:N.525, A:A.528 Water bridges: A:Y.124, A:T.529, A:T.529 BGC-GLC.2: 12 residues within 4Å: Chain B: S.122, Y.124, A.125, R.359, D.361, H.460, D.461, N.525, P.527, A.528, W.534 Ligands: EDO.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.359, B:H.460, B:H.460, B:N.525, B:S.122, B:D.461, B:N.525, B:A.528 Water bridges: B:R.359

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: T.176, F.249, L.252, F.253, K.256 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: A.129, N.130, M.282, R.347 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: P.283, I.284, Y.285, D.361, H.362 Ligands: BGC-GLC.1 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain A: P.230, A.238 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: A.351, Q.352, Y.355, D.356, E.357, C.358, I.403, K.404 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: D.208, Y.211, R.234 Ligand excluded by PLIP EDO.9: 10 residues within 4Å: Chain A: T.459, H.460, N.462, T.464, P.511, Q.513, D.514, R.523, M.524 Ligands: EDO.10 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: L.75, H.460, P.511, M.512, Q.513, M.524 Ligands: EDO.9 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: T.176, F.249, L.252, F.253, K.256 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain B: P.283, I.284, Y.285, W.326, D.361, H.362 Ligands: BGC-GLC.2 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain B: A.129, N.130, M.282, R.347, R.350, A.351, Y.355 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain B: A.351, Q.352, Y.355, D.356, E.357, C.358, I.403, K.404 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: E.207, D.208, Y.211, R.234 Ligand excluded by PLIP EDO.16: 10 residues within 4Å: Chain B: T.459, H.460, N.462, T.464, P.511, Q.513, D.514, R.523, M.524 Ligands: EDO.18 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain B: S.520, S.521, R.523, M.524, N.525, T.526, G.532, N.533 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: L.75, L.76, H.460, M.512, Q.513, M.524 Ligands: EDO.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

O'Neill, E.C. et al., Structural Dissection of the Maltodextrin Disproportionation Cycle of the Arabidopsis Plastidial Disproportionating Enzyme 1 (DPE1). J.Biol.Chem. (2015)

Release Date

2015-11-04

Peptides

4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

4-alpha-glucanotransferase DPE1, chloroplastic/amyloplastic

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