SMTL ID : 6lx1.1

Potato D-enzyme complexed with Acarbose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

homo-dimer

Ligands

2 x ASO- AC1: 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-1,5-anhydro-D-glucitol(Post Translational Modification)

ASO-AC1.1: 13 residues within 4Å: Chain A: S.82, Y.84, S.85, R.319, D.321, H.420, D.421, N.485, P.487, A.488, T.489, Q.490, W.494 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.84 Hydrogen bonds: A:S.82, A:N.485, A:A.488, A:T.489, A:Q.490, A:R.319, A:H.420, A:N.485 Water bridges: A:T.489, A:T.489, A:D.421 ASO-AC1.6: 13 residues within 4Å: Chain B: S.82, Y.84, S.85, R.319, D.321, H.420, D.421, N.485, P.487, A.488, T.489, Q.490, W.494 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.84 Hydrogen bonds: B:S.82, B:N.485, B:A.488, B:T.489, B:Q.490, B:R.319, B:H.420, B:N.485 Water bridges: B:T.489, B:T.489, B:R.319

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: T.181, I.182, S.183, D.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.182, A:S.183, A:D.186 GOL.3: 7 residues within 4Å: Chain A: R.426, S.453, R.454, I.457, D.474, G.477, K.513 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.426, A:R.426, A:K.513, A:K.513 Water bridges: A:S.453, A:R.454, A:R.454 GOL.7: 4 residues within 4Å: Chain B: T.181, I.182, S.183, D.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.182, B:S.183 GOL.8: 7 residues within 4Å: Chain B: R.426, S.453, R.454, I.457, D.474, G.477, K.513 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.426, B:R.426, B:K.513, B:K.513 Water bridges: B:S.453, B:R.454, B:R.454

2 x CA: CALCIUM ION(Non-covalent)

CA.4: 1 residues within 4Å: Chain A: N.180 No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain B: N.180 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: E.189, H.195 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.189, A:E.189, A:H.195 MG.10: 2 residues within 4Å: Chain B: E.189, H.195 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.189, B:E.189, B:H.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Imamura, K. et al., Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato. Protein Sci. (2020)

Release Date

2020-08-26

Peptides

4-alpha-glucanotransferase, chloroplastic/amyloplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

4-alpha-glucanotransferase, chloroplastic/amyloplastic

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