SMTL ID : 5jtt.1

Crystal structure of GPb in complex with 8a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.91, A:Y.649, A:V.651, A:K.681 Hydrogen bonds: A:T.677, A:G.678 Water bridges: A:G.136, A:K.569, A:K.569, A:K.575, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.4: 15 residues within 4Å: Chain B: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.91, B:Y.649, B:V.651, B:K.681 Hydrogen bonds: B:Y.649, B:T.677, B:G.678 Water bridges: B:G.136, B:K.569, B:K.569, B:K.575, B:N.679 Salt bridges: B:K.569, B:K.575

2 x 6MY: (1S)-1,5-anhydro-1-(5-phenyl-1H-imidazol-2-yl)-D-glucitol(Non-covalent)

6MY.2: 17 residues within 4Å: Chain A: E.89, G.136, L.137, L.140, N.283, N.285, F.286, H.342, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.485, A:Y.574, A:E.673, A:A.674, A:S.675, A:G.676 Water bridges: A:L.137, A:N.285, A:K.575, A:T.677 pi-Cation interactions: A:H.342 6MY.5: 17 residues within 4Å: Chain B: E.89, G.136, L.137, L.140, N.283, N.285, F.286, H.342, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.378, B:N.485, B:A.674, B:S.675, B:G.676 Water bridges: B:L.137, B:N.285, B:K.575, B:T.677 pi-Cation interactions: B:H.342

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 3 residues within 4Å: Chain A: R.243, R.310, R.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.310, A:R.310 DMS.6: 3 residues within 4Å: Chain B: R.243, R.310, R.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.310, B:R.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kantsadi, A.L. et al., Synthetic, enzyme kinetic, and protein crystallographic studies of C-beta-d-glucopyranosyl pyrroles and imidazoles reveal and explain low nanomolar inhibition of human liver glycogen phosphorylase. Eur.J.Med.Chem. (2016)

Release Date

2016-08-24

Peptides

Glycogen phosphorylase, muscle form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogen phosphorylase, muscle form

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