SMTL ID : 5lre.1

Crystal structure of Glycogen Phosphorylase b in complex with KS382

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x KS3: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(3-naphthalen-2-yl-1~{H}-1,2,4-triazol-5-yl)oxane-3,4,5-triol(Non-covalent)

KS3.1: 20 residues within 4Å: Chain A: E.88, G.135, L.136, L.139, N.282, N.284, F.285, F.286, R.292, H.341, H.377, T.378, A.383, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.284, A:N.484, A:E.672, A:A.673, A:S.674, A:G.675 Water bridges: A:L.136, A:D.283, A:K.574, A:T.676 pi-Cation interactions: A:H.341 KS3.2: 9 residues within 4Å: Chain A: R.60, V.64, W.67, P.188, W.189, E.190, K.191, A.192, P.229 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:R.60, A:V.64, A:W.67, A:K.191, A:K.191, A:P.229 Hydrogen bonds: A:R.60, A:R.60, A:E.190, A:K.191, A:A.192, A:A.192 pi-Cation interactions: A:R.60, A:K.191

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

PLP.3: 14 residues within 4Å: Chain A: G.134, G.135, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.648, A:V.650, A:K.680 Hydrogen bonds: A:T.676, A:G.677 Water bridges: A:G.135, A:K.568, A:K.568, A:K.574, A:N.678 Salt bridges: A:K.568, A:K.574

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

DMS.4: 3 residues within 4Å: Chain A: R.309, R.310 Ligands: DMS.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.309, A:R.309 DMS.5: 2 residues within 4Å: Chain A: Y.75 Ligands: DMS.4 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.75

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

2017-05-31

Peptides

Glycogen phosphorylase, muscle form: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycogen phosphorylase, muscle form

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