SMTL ID : 6r0i.1

Glycogen Phosphorylase b in complex with 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x JNB: ~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-4-phenyl-benzamide(Non-covalent)

JNB.1: 20 residues within 4Å: Chain A: G.136, L.137, L.140, N.283, D.284, N.285, F.286, F.287, R.293, H.342, H.378, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.137, A:L.137 Hydrogen bonds: A:G.136, A:L.137, A:N.285, A:N.285, A:N.485, A:N.485, A:E.673, A:E.673, A:A.674, A:S.675, A:G.676, A:G.676 Water bridges: A:G.138, A:T.677 pi-Cation interactions: A:H.342 JNB.3: 20 residues within 4Å: Chain B: G.136, L.137, L.140, N.283, D.284, N.285, F.286, F.287, R.293, H.342, H.378, A.384, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:L.137, B:L.137 Hydrogen bonds: B:G.136, B:L.137, B:N.285, B:N.285, B:H.378, B:N.485, B:N.485, B:Y.574, B:E.673, B:A.674, B:S.675, B:G.676, B:G.676 Water bridges: B:G.138, B:T.677 pi-Cation interactions: B:H.342

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

PLP.2: 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:T.677, A:G.678 Water bridges: A:Y.91, A:K.569, A:K.575, A:N.679, 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:T.677, B:T.677, B:G.678 Water bridges: B:K.569, B:K.575, B:Y.649, B:N.679, B:N.679 Salt bridges: B:K.569, B:K.575

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fischer, T. et al., High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-beta-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors. Molecules (2019)

Release Date

2019-04-17

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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