SMTL ID : 3amv.1

ALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ANTIDIABETIC DRUG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 11 residues within 4Å: Chain A: G.135, L.136, N.284, H.377, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.135, A:L.136, A:N.284, A:N.284, A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:D.283, A:D.283, A:Y.573, A:Y.573, A:Y.573, A:K.574 Salt bridges: A:H.377 GLC.5: 11 residues within 4Å: Chain B: G.135, L.136, N.284, H.377, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:G.135, B:L.136, B:N.284, B:N.284, B:H.377, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:D.283, B:D.283, B:Y.573, B:K.574, B:A.673 Salt bridges: B:H.377

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

PLP.2: 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 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.90, 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.568, A:K.574, A:K.574, A:G.675, A:G.675, 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 17 PLIP interactions: 17 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:G.135, B:K.568, B:K.568, B:K.574, B:K.574, B:G.675, B:G.675, B:N.678 Salt bridges: B:K.568, B:K.574

2 x BIN: 2,3-DICARBOXY-4-(2-CHLORO-PHENYL)-1-ETHYL-5-ISOPROPOXYCARBONYL-6-METHYL-PYRIDINIUM(Non-covalent)

BIN.3: 16 residues within 4Å: Chain A: W.67, I.68, Q.71, Q.72, Y.75, R.81, R.193, E.195, F.196, D.227, R.242, R.309, R.310 Chain B: V.40, K.41, V.45 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Q.71, A:Q.71, A:Y.75, A:Y.75, A:F.196, A:F.196, B:V.45, B:V.45 Hydrogen bonds: A:R.81 Water bridges: A:Q.71, A:Q.72, A:R.309 Salt bridges: A:R.242, A:R.309, A:R.309, A:R.310, A:R.310 Halogen bonds: A:R.193 BIN.7: 16 residues within 4Å: Chain A: V.40, K.41, V.45 Chain B: W.67, I.68, Q.71, Q.72, Y.75, R.81, R.193, E.195, F.196, D.227, R.242, R.309, R.310 18 PLIP interactions: 16 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.71, B:Q.71, B:Y.75, B:Y.75, B:F.196, B:F.196, A:V.45, A:V.45 Hydrogen bonds: B:R.81 Water bridges: B:Q.71, B:Q.72, B:R.309 Salt bridges: B:R.242, B:R.309, B:R.309, B:R.310, B:R.310 Halogen bonds: B:R.193

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: Y.726, H.767, H.768, D.769, R.770 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.769, A:K.772 GOL.8: 5 residues within 4Å: Chain B: Y.726, H.767, H.768, D.769, R.770 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.769, B:K.772

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oikonomakos, N.G. et al., Allosteric inhibition of glycogen phosphorylase a by the potential antidiabetic drug 3-isopropyl 4-(2-chlorophenyl)-1,4-dihydro-1-ethyl-2-methyl-pyridine-3,5,6-tricarbo xylate. Protein Sci. (1999)

Release Date

1999-02-26

Peptides

PROTEIN (GLYCOGEN PHOSPHORYLASE): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PROTEIN (GLYCOGEN PHOSPHORYLASE)

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