SMTL ID : 1xc7.1

Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: Kinetic and crystallographic studies

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x GL6: N-(dimethoxyphosphoryl)-beta-D-glucopyranosylamine(Non-covalent)

GL6.1: 15 residues within 4Å: Chain A: G.135, L.136, L.139, D.283, F.285, D.339, H.377, T.378, 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:H.377, A:H.377, A:Y.573, A:E.672, A:E.672, A:S.674, A:G.675, A:G.675 Water bridges: A:N.284, A:A.673, A:T.676 GL6.4: 15 residues within 4Å: Chain B: G.135, L.136, L.139, D.283, F.285, D.339, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:H.377, B:H.377, B:H.377, B:E.672, B:S.674, B:G.675, B:G.675 Water bridges: B:N.284, B:A.673, B:T.676

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: F.196, R.242, R.309, R.310 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.227, A:R.310 Salt bridges: A:R.242, A:R.309, A:R.310 SO4.5: 4 residues within 4Å: Chain B: F.196, R.242, R.309, R.310 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.242, B:R.310 Salt bridges: B:R.242, B:R.309, B:R.310

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

PLP.3: 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:V.650, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:G.677 Water bridges: A:G.135, A:K.568, A:K.574, A:N.678, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.6: 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 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.90, B:Y.648, B:V.650, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:T.676, B:G.677 Water bridges: B:G.135, B:K.568, B:K.574, B:N.678, B:N.678 Salt bridges: B:K.568, B:K.574

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chrysina, E.D. et al., Binding of beta-d-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: kinetic and crystallographic studies. Bioorg.Med.Chem. (2005)

Release Date

2005-02-08

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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