SMTL ID : 2f3q.1

Crystal structure of the glycogen phosphorylase B / methyl-N-(beta-D-glucopyranosyl)oxamate complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: Y.90, 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 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:G.677 Water bridges: A:Y.90, A:G.135, A:K.568, A:K.574, A:K.574, A:K.574, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.3: 15 residues within 4Å: Chain B: Y.90, 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.90, B:Y.648, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:G.677 Water bridges: B:G.135, B:K.568, B:K.574, B:K.574, B:K.574, B:N.678 Salt bridges: B:K.568, B:K.574

2 x 6GP: N-[methoxy(oxo)acetyl]-beta-D-glucopyranosylamine(Non-covalent)

6GP.2: 16 residues within 4Å: Chain A: G.135, L.136, L.139, D.283, N.284, D.339, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675, T.676 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:L.136, A:N.284, A:N.284, A:N.284, A:H.377, A:N.484, A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:G.135, A:G.137, A:D.283, A:Y.573, A:K.574, A:A.673, A:A.673, A:T.676 6GP.4: 16 residues within 4Å: Chain B: G.135, L.136, L.139, D.283, N.284, D.339, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675, T.676 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:L.136, B:N.284, B:N.284, B:N.284, B:H.377, B:H.377, B:N.484, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:G.135, B:G.137, B:K.574, B:A.673, B:A.673, B:T.676

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hadjiloi, T. et al., Binding of oxalyl derivatives of beta-d-glucopyranosylamine to muscle glycogen phosphorylase b. Bioorg.Med.Chem. (2006)

Release Date

2006-05-09

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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