SMTL ID : 5mem.1

A potent fluorescent inhibitor of glycogen phosphorylase as a catalytic site probe.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 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 14 PLIP interactions: 14 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:Y.91, A:G.136, A:K.569, A:K.569, A:K.575, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.3: 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 15 PLIP interactions: 15 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, B:K.681 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 7LS: 2-[[1-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-10~{H}-acridin-9-one(Non-covalent)

7LS.2: 24 residues within 4Å: Chain A: E.89, G.136, L.137, L.140, Y.281, N.283, D.284, N.285, F.286, F.287, E.288, R.293, D.340, H.342, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:Y.281, A:N.283, A:F.287, A:R.293, A:H.378, A:T.379 Hydrogen bonds: A:E.89, A:E.89, A:G.136, A:L.137, A:N.285, A:N.285, A:D.340, A:N.485, A:Y.574, A:E.673, A:A.674, A:S.675, A:G.676 Water bridges: A:N.134, A:G.138, A:R.293, A:R.293, A:T.677 pi-Stacking: A:H.342 pi-Cation interactions: A:R.293 7LS.4: 24 residues within 4Å: Chain B: E.89, G.136, L.137, L.140, Y.281, N.283, D.284, N.285, F.286, F.287, E.288, R.293, D.340, H.342, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:Y.281, B:N.283, B:F.287, B:R.293, B:H.378, B:T.379 Hydrogen bonds: B:E.89, B:G.136, B:L.137, B:N.285, B:N.285, B:D.340, B:H.378, B:N.485, B:A.674, B:S.675, B:G.676 Water bridges: B:N.134, B:G.138, B:R.293, B:R.293, B:T.677 pi-Stacking: B:H.342 pi-Cation interactions: B:R.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mamais, M. et al., A New Potent Inhibitor of Glycogen Phosphorylase Reveals the Basicity of the Catalytic Site. Chemistry (2017)

Release Date

2017-11-29

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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