SMTL ID : 2qn8.1

Glycogen Phosphorylase b in complex with N-4-nitrobenzoyl-N'-beta-D-glucopyranosyl urea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: F.196, R.242, R.309, R.310 3 PLIP interactions: 3 interactions with chain A 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 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.155 Salt bridges: 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, 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:Y.90, A:G.135, 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 14 PLIP interactions: 14 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.574, B:N.678, B:N.678 Salt bridges: B:K.568, B:K.574

4 x NBY: N-{[(4-nitrophenyl)carbonyl]carbamoyl}-beta-D-glucopyranosylamine(Non-covalent)

NBY.3: 18 residues within 4Å: Chain A: R.60, L.63, V.64, W.67, P.188, W.189, E.190, K.191, P.229 Chain B: F.37, T.38, L.39, V.40, F.53, H.57, R.60, P.188 Ligands: NBY.7 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:V.40, A:V.64, A:W.67, A:K.191 Hydrogen bonds: B:T.38, B:H.57, B:R.60, A:E.190 pi-Cation interactions: A:R.60 NBY.4: 19 residues within 4Å: Chain A: E.88, N.133, G.135, L.136, L.139, N.282, D.283, F.285, F.286, H.341, H.377, A.383, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:D.283 Hydrogen bonds: A:L.136, A:A.383, A:N.484, A:Y.573, A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:G.135, A:G.137, A:H.377, A:T.378, A:Y.573, A:A.673, A:T.676 NBY.7: 18 residues within 4Å: Chain A: F.37, T.38, L.39, V.40, F.53, H.57, R.60, P.188 Chain B: R.60, L.63, V.64, W.67, P.188, W.189, E.190, K.191, P.229 Ligands: NBY.3 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.64, B:W.67, B:K.191, A:V.40 Hydrogen bonds: B:E.190, A:T.38, A:H.57, A:R.60 pi-Cation interactions: B:R.60 NBY.8: 19 residues within 4Å: Chain B: E.88, N.133, G.135, L.136, L.139, N.282, D.283, F.285, F.286, H.341, H.377, A.383, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:D.283 Hydrogen bonds: B:L.136, B:H.377, B:A.383, B:N.484, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:G.135, B:G.137, B:H.377, B:T.378, B:Y.573, B:Y.573, B:Y.573, B:A.673, B:T.676

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagy, V. et al., N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation. To be Published

Release Date

2008-07-22

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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