SMTL ID : 5csu.1

Disproportionating enzyme 1 from Arabidopsis - acarviostatin soak

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

2 x GLC- AGL: 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-AGL.1: 11 residues within 4Å: Chain A: S.122, Y.124, L.325, W.326, D.461, N.525, P.527, A.528, T.529 Ligands: HMC.7, HMC.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.326, A:A.528, A:T.529, A:T.529, A:S.122, A:D.461, A:N.525, A:A.528 Water bridges: A:T.529 GLC-AGL.3: 11 residues within 4Å: Chain B: S.122, Y.124, L.325, W.326, D.461, N.525, P.527, A.528, T.529 Ligands: HMC.10, HMC.11 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.326, B:A.528, B:T.529, B:T.529, B:S.122, B:D.461, B:N.525, B:A.528 Water bridges: B:T.529

2 x BGC- GLC- AGL: 4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose

BGC-GLC-AGL.2: 12 residues within 4Å: Chain A: D.317, L.318, F.319, Q.324, H.362, E.408, L.410, G.411, F.434, H.444, D.461 Ligands: HMC.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.324, A:H.362, A:H.362, A:E.408, A:L.410, A:D.317, A:L.318, A:Q.324, A:G.411 Water bridges: A:R.359, A:L.410, A:L.410, A:V.412, A:V.412, A:T.459, A:T.459 Salt bridges: A:H.444 BGC-GLC-AGL.4: 12 residues within 4Å: Chain B: D.317, L.318, F.319, Q.324, H.362, E.408, L.410, G.411, F.434, H.444, D.461 Ligands: HMC.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.324, B:H.362, B:H.362, B:E.408, B:L.410, B:L.318, B:Q.324, B:G.411 Water bridges: B:L.410, B:L.410 Salt bridges: B:H.444

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

EDO.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.6: 8 residues within 4Å: Chain A: A.351, Q.352, Y.355, D.356, E.357, C.358, I.403, K.404 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.351, A:Q.352, A:K.404 EDO.9: 5 residues within 4Å: Chain B: S.521, R.523, T.526, G.532, N.533 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.526, B:T.526, B:N.533

4 x HMC: 5-HYDROXYMETHYL-CHONDURITOL(Non-covalent)

HMC.7: 4 residues within 4Å: Chain A: L.325, W.326, G.327 Ligands: GLC-AGL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.326 HMC.8: 10 residues within 4Å: Chain A: Y.124, W.326, R.359, D.361, E.408, H.460, D.461, W.534 Ligands: GLC-AGL.1, BGC-GLC-AGL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.359, A:D.361, A:D.461, A:N.525 Water bridges: A:D.461 HMC.10: 3 residues within 4Å: Chain B: L.325, G.327 Ligands: GLC-AGL.3 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.325 HMC.11: 9 residues within 4Å: Chain B: Y.124, W.326, R.359, D.361, E.408, H.460, D.461 Ligands: GLC-AGL.3, BGC-GLC-AGL.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.124, B:R.359, B:D.361, B:D.461, B:N.525

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

Related Entries With Identical Sequence