SMTL ID : 1axr.1

COOPERATIVITY BETWEEN HYDROGEN-BONDING AND CHARGE-DIPOLE INTERACTIONS IN THE INHIBITION OF BETA-GLYCOSIDASES BY AZOLOPYRIDINES: EVIDENCE FROM A STUDY WITH GLYCOGEN PHOSPHORYLASE B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: Y.75, Y.155, R.309, R.310 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.75, A:Y.75, A:Y.75, A:R.242 Water bridges: A:R.309 Salt bridges: A:R.309, A:R.310 PO4.2: 8 residues within 4Å: Chain A: G.135, L.136, R.569, Y.573, K.574, E.672 Ligands: PLP.3, HTP.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.135, A:L.136, A:Y.573, A:E.672 Water bridges: A:N.284, A:R.569, A:K.574, A:G.675 Salt bridges: A:R.569, A:K.574 PO4.5: 4 residues within 4Å: Chain B: Y.75, Y.155, R.309, R.310 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.75, B:Y.75, B:Y.155, B:R.242 Water bridges: B:Y.75, B:Y.75, B:R.309 Salt bridges: B:R.309, B:R.310 PO4.6: 8 residues within 4Å: Chain B: G.135, L.136, R.569, Y.573, K.574, E.672 Ligands: PLP.7, HTP.8 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.135, B:L.136, B:Y.573, B:E.672 Water bridges: B:N.284, B:R.569, B:K.574, B:G.675 Salt bridges: B:R.569, B:K.574

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

PLP.3: 16 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 Ligands: PO4.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:Y.90, A:R.138, A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:G.677 Water bridges: A:Y.90, A:K.568, A:K.568, A:K.574, A:K.574, A:G.675, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.7: 16 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 Ligands: PO4.6 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:Y.90, B:R.138, B:Y.648, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:G.677 Water bridges: B:K.568, B:K.568, B:K.574, B:K.574, B:G.675, B:N.678 Salt bridges: B:K.568, B:K.574

2 x HTP: 4,5,6-TRIHYDROXY-7-HYDROXYMETHYL-4,5,6,7-TETRAHYDRO-1H-[1,2,3]TRIAZOLO[1,5-A]PYRIDIN-8-YLIUM(Non-covalent)

HTP.4: 14 residues within 4Å: Chain A: G.135, L.136, L.139, N.284, H.377, V.455, N.484, R.569, Y.573, E.672, A.673, S.674, G.675 Ligands: PO4.2 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.284, A:H.377, A:R.569, A:Y.573, A:E.672, A:E.672, A:A.673, A:S.674, A:S.674, A:G.675 HTP.8: 14 residues within 4Å: Chain B: G.135, L.136, L.139, N.284, H.377, V.455, N.484, R.569, Y.573, E.672, A.673, S.674, G.675 Ligands: PO4.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.284, B:H.377, B:H.377, B:R.569, B:E.672, B:A.673, B:S.674, B:S.674, B:G.675 Water bridges: B:Y.573

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heightman, T.D. et al., Cooperative interactions of the catalytic nucleophile and the catalytic acid in the inhibition of beta-glycosidases. Calculations and their validation by comparative kinetic and structural studies of the inhibition of glycogen phosphorylase b. HELV.CHIM.ACTA (1998)

Release Date

1998-01-28

Peptides

GLYCOGEN PHOSPHORYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYCOGEN PHOSPHORYLASE

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