SMTL ID : 3cem.1

Human glycogen phosphorylase (tense state) in complex with the allosteric inhibitor AVE9423

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.47 Å

Oligo State

homo-dimer

Ligands

2 x NBG: N-acetyl-beta-D-glucopyranosylamine(Non-covalent)

NBG.1: 12 residues within 4Å: Chain A: G.113, L.114, L.117, N.262, H.355, V.433, N.462, Y.551, E.650, A.651, S.652, G.653 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.262, A:H.355, A:H.355, A:N.462, A:N.462, A:Y.551, A:E.650, A:E.650, A:S.652, A:G.653, A:G.653 Water bridges: A:A.651, A:A.651 NBG.4: 13 residues within 4Å: Chain B: G.113, L.114, L.117, N.262, D.317, H.355, V.433, N.462, Y.551, E.650, A.651, S.652, G.653 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.114 Hydrogen bonds: B:N.262, B:H.355, B:N.462, B:N.462, B:Y.551, B:E.650, B:S.652, B:G.653, B:G.653 Water bridges: B:A.651, B:T.654

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

PLP.2: 15 residues within 4Å: Chain A: Y.68, G.112, G.113, R.116, W.469, K.546, K.552, Y.626, R.627, V.628, A.631, G.653, T.654, G.655, K.658 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.68, A:Y.626, A:V.628 Hydrogen bonds: A:T.654, A:T.654, A:G.655 Water bridges: A:G.113, A:V.545, A:K.546, A:K.546, A:N.656 Salt bridges: A:K.546, A:K.552 PLP.5: 14 residues within 4Å: Chain B: Y.68, G.112, G.113, W.469, K.546, K.552, Y.626, R.627, V.628, A.631, G.653, T.654, G.655, K.658 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.68, B:Y.626, B:V.628 Hydrogen bonds: B:Q.643, B:T.654, B:G.655, B:K.658 Water bridges: B:Y.68, B:G.113, B:K.546, B:K.546 Salt bridges: B:K.546, B:K.552

2 x AVD: 1-(2-carboxyphenyl)-7-chloro-6-[(2-chloro-4,6-difluorophenyl)amino]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid(Non-covalent)

AVD.3: 15 residues within 4Å: Chain A: W.45, I.46, Q.49, Y.53, K.169, R.171, F.174, D.205, R.220, R.287, R.288 Chain B: L.17, V.18, K.19, V.23 15 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Y.53, A:Y.53, B:V.18, B:V.18, B:V.23, B:V.23 Hydrogen bonds: A:R.171, A:R.171, A:R.220, B:V.18 Salt bridges: A:R.220, A:R.287, A:R.288 pi-Stacking: A:W.45 Halogen bonds: A:W.45 AVD.6: 15 residues within 4Å: Chain A: L.17, V.18, K.19, V.23 Chain B: W.45, I.46, Q.49, Y.53, K.169, R.171, F.174, D.205, R.220, R.287, R.288 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:Y.53, A:V.18, A:V.18, A:V.23, A:V.23 Hydrogen bonds: B:R.171, B:R.171, B:R.220, A:V.18 Salt bridges: B:R.220, B:R.287, B:R.288 pi-Stacking: B:W.45, B:Y.53 Halogen bonds: B:W.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Anderka, O. et al., Thermodynamic characterization of allosteric glycogen phosphorylase inhibitors. Biochemistry (2008)

Release Date

2008-05-27

Peptides

Glycogen phosphorylase, liver form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glycogen phosphorylase, liver form

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