SMTL ID : 1l5r.1

Human liver glycogen phosphorylase a complexed with riboflavin, N-Acetyl-beta-D-Glucopyranosylamine and CP-403,700

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NBG.1: 14 residues within 4Å: Chain A: G.136, L.137, L.140, N.285, D.340, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:H.378, A:T.379 Hydrogen bonds: A:N.285, A:N.285, A:H.378, A:H.378, A:N.485, A:N.485, A:E.673, A:E.673, A:S.675, A:S.675, A:G.676 Water bridges: A:L.137, A:N.285, A:Y.574, A:A.674, A:A.674, A:T.677 NBG.7: 14 residues within 4Å: Chain C: G.136, L.137, L.140, N.285, D.340, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:H.378, C:T.379 Hydrogen bonds: C:N.285, C:N.285, C:H.378, C:H.378, C:N.485, C:N.485, C:E.673, C:E.673, C:S.675, C:S.675, C:G.676 Water bridges: C:L.137, C:N.285, C:Y.574, C:A.674, C:A.674, C:T.677

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

PLP.2: 16 residues within 4Å: Chain A: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, Q.666, G.676, T.677, G.678, K.681 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.91, A:Y.649, A:K.681 Hydrogen bonds: A:V.568, A:T.677, A:T.677, A:G.678 Water bridges: A:G.136, A:G.676, A:N.679, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.5: 15 residues within 4Å: Chain B: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:Y.91, B:Y.649, B:V.651, B:K.681 Hydrogen bonds: B:V.568, B:Y.649, B:T.677, B:T.677, B:G.678 Water bridges: B:Y.91, B:K.569, B:K.569, B:K.575, B:N.679 Salt bridges: B:K.569, B:K.575 PLP.8: 16 residues within 4Å: Chain C: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, Q.666, G.676, T.677, G.678, K.681 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:Y.91, C:Y.649, C:K.681 Hydrogen bonds: C:V.568, C:T.677, C:T.677, C:G.678 Water bridges: C:G.136, C:G.676, C:N.679, C:N.679 Salt bridges: C:K.569, C:K.575 PLP.11: 15 residues within 4Å: Chain D: Y.91, G.135, G.136, W.492, V.568, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:Y.91, D:Y.649, D:V.651, D:K.681 Hydrogen bonds: D:V.568, D:Y.649, D:T.677, D:T.677, D:G.678 Water bridges: D:Y.91, D:K.569, D:K.569, D:K.575, D:N.679 Salt bridges: D:K.569, D:K.575

2 x 700: [5-CHLORO-1H-INDOL-2-CARBONYL-PHENYLALANINYL]-AZETIDINE-3-CARBOXYLIC ACID(Non-covalent)

700.3: 18 residues within 4Å: Chain A: R.61, L.64, V.65, W.68, P.189, W.190, E.191, K.192, S.193, P.230 Chain B: T.39, V.41, F.54, H.58, R.185, Y.186, N.188, P.189 19 PLIP interactions: 7 interactions with chain B, 12 interactions with chain A Hydrophobic interactions: B:T.39, B:V.41, B:P.189, A:W.68, A:K.192, A:K.192, A:P.230 Hydrogen bonds: B:T.39, B:Y.186, A:K.192, A:S.193 pi-Stacking: B:F.54, B:H.58 Water bridges: A:R.61, A:R.61, A:R.61, A:S.193, A:Y.227 pi-Cation interactions: A:R.61 700.9: 18 residues within 4Å: Chain C: R.61, L.64, V.65, W.68, P.189, W.190, E.191, K.192, S.193, P.230 Chain D: T.39, V.41, F.54, H.58, R.185, Y.186, N.188, P.189 19 PLIP interactions: 7 interactions with chain D, 12 interactions with chain C Hydrophobic interactions: D:T.39, D:V.41, D:P.189, C:W.68, C:K.192, C:K.192, C:P.230 Hydrogen bonds: D:T.39, D:Y.186, C:K.192, C:S.193 pi-Stacking: D:F.54, D:H.58 Water bridges: C:R.61, C:R.61, C:R.61, C:S.193, C:Y.227 pi-Cation interactions: C:R.61

2 x RBF: RIBOFLAVIN(Non-covalent)

RBF.4: 13 residues within 4Å: Chain A: N.283, D.284, N.285, F.286, L.381, E.383, H.572, Y.574, A.611, G.613, Y.614, R.771, F.772 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.381, A:E.383, A:Y.574, A:Y.614, A:F.772 Hydrogen bonds: A:E.573, A:R.771 Water bridges: A:N.283, A:D.284, A:Y.614, A:H.615, A:H.615, A:H.615 pi-Stacking: A:F.286, A:Y.614 RBF.10: 13 residues within 4Å: Chain C: N.283, D.284, N.285, F.286, L.381, E.383, H.572, Y.574, A.611, G.613, Y.614, R.771, F.772 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.381, C:E.383, C:Y.574, C:Y.614, C:F.772 Hydrogen bonds: C:E.573, C:R.771 Water bridges: C:N.283, C:D.284, C:Y.614, C:H.615, C:H.615, C:H.615 pi-Stacking: C:F.286, C:Y.614

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.6: 7 residues within 4Å: Chain A: V.41, K.42, V.46 Chain B: W.68, I.69, Q.72, R.194 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:V.41, B:W.68, B:W.68, B:Q.72 Hydrogen bonds: A:V.41, B:R.194 Water bridges: B:D.228, B:R.243 MRD.12: 7 residues within 4Å: Chain C: V.41, K.42, V.46 Chain D: W.68, I.69, Q.72, R.194 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.68, D:W.68, D:Q.72, C:V.41 Hydrogen bonds: D:R.194, C:V.41 Water bridges: D:D.228, D:R.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ekstrom, J.L. et al., Structure-activity analysis of the purine binding site of human liver glycogen phosphorylase. Chem.Biol. (2002)

Release Date

2002-12-04

Peptides

glycogen phosphorylase, liver form: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

glycogen phosphorylase, liver form

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