SMTL ID : 3ceh.1

Human liver glycogen phosphorylase (tense state) in complex with the allosteric inhibitor AVE5688

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

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

NBG.1: 14 residues within 4Å: Chain A: G.113, L.114, L.117, D.261, N.262, H.355, V.433, N.462, Y.551, E.650, A.651, S.652, G.653, T.654 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.114, A:H.355 Hydrogen bonds: A:N.262, A:H.355, A:H.355, A:H.355, A:N.462, A:E.650, A:A.651, A:S.652, A:G.653, A:G.653 Water bridges: A:N.262 NBG.5: 14 residues within 4Å: Chain B: G.113, L.114, L.117, N.262, H.355, T.356, V.433, N.462, Y.551, E.650, A.651, S.652, G.653, T.654 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:T.356 Hydrogen bonds: B:L.114, B:N.262, 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:K.552

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

PO4.2: 5 residues within 4Å: Chain A: R.171, F.174, R.220, R.288 Ligands: AVE.4 9 PLIP interactions: 9 interactions with chain A Water bridges: A:Q.49, A:Y.133, A:R.171, A:R.171, A:R.171, A:R.171 Salt bridges: A:R.171, A:R.220, A:R.288 PO4.6: 5 residues within 4Å: Chain B: F.174, R.220, R.287, R.288 Ligands: AVE.9 7 PLIP interactions: 7 interactions with chain B Water bridges: B:R.171, B:R.171, B:R.171 Salt bridges: B:R.171, B:R.220, B:R.287, B:R.288

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

PLP.3: 15 residues within 4Å: Chain A: Y.68, G.112, G.113, W.469, V.545, K.546, K.552, Y.626, R.627, V.628, A.631, G.653, T.654, G.655, K.658 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.626 Hydrogen bonds: A:T.654, A:T.654, A:G.655 Water bridges: A:G.113, A:V.545, A:K.552, A:N.656 Salt bridges: A:K.546, A:K.552 PLP.8: 16 residues within 4Å: Chain B: Y.68, G.112, G.113, R.116, W.469, V.545, 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 Hydrogen bonds: B:Y.626, B:T.654, B:G.655, B:K.658 Water bridges: B:V.545, B:K.552, B:K.552, B:Q.643, B:T.654 Salt bridges: B:K.546, B:K.552

2 x AVE: 4-[3-(2-Chloro-4,5-difluoro-benzoyl)ureido]-3-trifluoromethoxybenzoic acid(Non-covalent)

AVE.4: 15 residues within 4Å: Chain A: W.45, I.46, Q.49, Q.50, Y.53, K.169, R.171, D.205 Chain B: L.17, V.18, K.19, D.20, N.22, V.23 Ligands: PO4.2 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:V.18, B:K.19, A:I.46, A:Q.50 Hydrogen bonds: B:V.18, B:D.20, B:N.22, A:Q.50 Water bridges: A:R.171 pi-Stacking: A:W.45 Halogen bonds: A:W.45 AVE.9: 15 residues within 4Å: Chain A: L.17, V.18, K.19, D.20, N.22, V.23 Chain B: W.45, I.46, Q.49, Q.50, Y.53, K.169, R.171, D.205 Ligands: PO4.6 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.18, A:V.23, A:V.23, B:I.46 Hydrogen bonds: A:V.18, A:D.20, A:N.22, B:Q.50 Water bridges: B:R.171, B:R.171 pi-Stacking: B:W.45 Halogen bonds: B:W.45

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 7 residues within 4Å: Chain B: R.27, R.71, E.102, I.103, E.104, E.105, R.627 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.71, B:E.102, B:R.627 Salt bridges: B:R.27, B:E.105

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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