SMTL ID : 1k08.1

Crystallographic Binding Study of 10 mM N-benzoyl-N'-beta-D-glucopyranosyl urea to glycogen phosphorylase b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

4 x BZD: N-[(phenylcarbonyl)carbamoyl]-beta-D-glucopyranosylamine(Non-covalent)

BZD.1: 16 residues within 4Å: Chain A: E.88, N.133, G.135, L.136, L.139, N.282, D.283, H.341, H.377, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.136, A:Y.573, A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:G.134, A:G.134, A:G.135, A:G.135, A:G.135, A:D.339, A:H.377, A:A.673, A:T.676 pi-Cation interactions: A:H.341 BZD.2: 14 residues within 4Å: Chain A: R.60, V.64, W.67, P.188, W.189, E.190, K.191, P.229 Chain B: F.37, T.38, L.39, V.40, H.57 Ligands: BZD.5 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:V.40, A:R.60, A:V.64, A:W.67, A:P.229 Hydrogen bonds: B:T.38, B:H.57, B:R.60, A:R.60, A:E.190, A:K.191 BZD.4: 16 residues within 4Å: Chain B: E.88, N.133, G.135, L.136, L.139, N.282, D.283, H.341, H.377, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:L.136, B:H.377, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:G.134, B:G.134, B:G.135, B:G.135, B:G.135, B:D.339, B:H.377, B:Y.573, B:Y.573, B:A.673, B:T.676 pi-Cation interactions: B:H.341 BZD.5: 14 residues within 4Å: Chain A: F.37, T.38, L.39, V.40, H.57 Chain B: R.60, V.64, W.67, P.188, W.189, E.190, K.191, P.229 Ligands: BZD.2 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:R.60, B:V.64, B:W.67, B:P.229, A:V.40 Hydrogen bonds: B:R.60, B:E.190, B:K.191, A:T.38, A:H.57, A:R.60

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

PLP.3: 14 residues within 4Å: Chain A: Y.90, G.134, G.135, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:G.677 Water bridges: A:K.568, A:K.568, A:K.574, A:K.574, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.6: 14 residues within 4Å: Chain B: Y.90, G.134, G.135, W.491, 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:T.676, B:G.677 Water bridges: B:K.568, B:K.568, B:K.574, B:K.574, B:N.678 Salt bridges: B:K.568, B:K.574

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oikonomakos, N.G. et al., Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies. Eur.J.Biochem. (2002)

Release Date

2001-10-03

Peptides

Glycogen Phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glycogen Phosphorylase

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