SMTL ID : 2pri.1

BINDING OF 2-DEOXY-GLUCOSE-6-PHOSPHATE TO GLYCOGEN PHOSPHORYLASE B

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x D6G: 2-deoxy-6-O-phosphono-alpha-D-glucopyranose(Non-covalent)

D6G.1: 10 residues within 4Å: Chain A: W.67, I.68, Q.71, Y.75, R.193, D.227, R.242, R.309, R.310 Chain B: V.40 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.67 Hydrogen bonds: A:D.227, B:V.40 Water bridges: A:R.310 Salt bridges: A:R.193, A:R.242, A:R.309, A:R.310 D6G.3: 10 residues within 4Å: Chain A: V.40 Chain B: W.67, I.68, Q.71, Y.75, R.193, D.227, R.242, R.309, R.310 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.67 Hydrogen bonds: B:Y.75, A:V.40 Water bridges: B:T.240, B:R.310 Salt bridges: B:R.193, B:R.242, B:R.309, B:R.310

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

PLP.2: 15 residues within 4Å: Chain A: Y.90, G.134, G.135, R.138, W.491, 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 A Hydrophobic interactions: A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:T.676, A:G.677 Water bridges: A:Y.90, A:G.135, A:K.568, A:K.574, A:G.675, A:N.678, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.4: 15 residues within 4Å: Chain B: Y.90, G.134, G.135, R.138, 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.648, B:K.680 Hydrogen bonds: B:T.676, B:T.676, B:G.677 Water bridges: B:G.135, B:K.568, B:K.574, B:Y.648, B:G.675, B:N.678, 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., The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies. J.Mol.Biol. (1995)

Release Date

1998-12-14

Peptides

GLYCOGEN PHOSPHORYLASE B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYCOGEN PHOSPHORYLASE B

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