SMTL ID : 1l5s.1

Human liver glycogen phosphorylase complexed with uric acid, N-Acetyl-beta-D-glucopyranosylamine, and CP-403,700

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NBG.1: 13 residues within 4Å: Chain A: G.136, L.137, N.285, D.340, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: 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 NBG.8: 15 residues within 4Å: Chain B: 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, T.677 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:L.137, B:H.378, B:T.379 Hydrogen bonds: B:N.285, B:N.285, B:H.378, B:N.485, B:N.485, B:E.673, B:S.675, B:S.675, B:G.676 Water bridges: B:L.137, B:N.285, B:T.379, B:K.575, B:K.575, B:K.575, B:A.674, B:T.677 NBG.14: 13 residues within 4Å: Chain C: G.136, L.137, N.285, D.340, H.378, T.379, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: 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 NBG.21: 15 residues within 4Å: Chain D: 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, T.677 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:L.137, D:H.378, D:T.379 Hydrogen bonds: D:N.285, D:N.285, D:H.378, D:N.485, D:N.485, D:E.673, D:S.675, D:S.675, D:G.676 Water bridges: D:L.137, D:N.285, D:T.379, D:K.575, D:K.575, D:K.575, D:A.674, D:T.677

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

PLP.2: 15 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, G.676, T.677, G.678, K.681 14 PLIP interactions: 14 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:K.569, A:K.575, A:N.679, A:N.679 Salt bridges: A:K.569, A:K.575 PLP.9: 14 residues within 4Å: Chain B: Y.91, G.135, G.136, W.492, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.91, B:Y.649, 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:G.136, B:K.569, B:K.575, B:K.575, B:N.679, B:N.679 Salt bridges: B:K.569, B:K.575 PLP.15: 15 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, G.676, T.677, G.678, K.681 14 PLIP interactions: 14 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:K.569, C:K.575, C:N.679, C:N.679 Salt bridges: C:K.569, C:K.575 PLP.22: 14 residues within 4Å: Chain D: Y.91, G.135, G.136, W.492, K.569, K.575, Y.649, R.650, V.651, A.654, G.676, T.677, G.678, K.681 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:Y.91, D:Y.649, 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:G.136, D:K.569, D:K.575, D:K.575, D:N.679, D:N.679 Salt bridges: D:K.569, D:K.575

4 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, Y.186, G.187, N.188, P.189 20 PLIP interactions: 6 interactions with chain B, 14 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, A:K.192, A:S.193, A:S.193, A:Y.227 pi-Stacking: B:F.54, B:H.58 Water bridges: A:R.61, A:R.61, A:R.61, A:S.193, A:S.193 pi-Cation interactions: A:R.61 700.10: 18 residues within 4Å: Chain A: T.39, V.41, F.54, H.58, Y.186, G.187, N.188, P.189 Chain B: R.61, L.64, V.65, W.68, P.189, W.190, E.191, K.192, S.193, P.230 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:W.68, B:K.192, B:K.192, A:T.39, A:V.41, A:P.189 Hydrogen bonds: B:K.192, A:T.39 Water bridges: B:R.61, B:R.61, B:R.61, B:S.193, B:S.193, A:Y.186 pi-Cation interactions: B:R.61 pi-Stacking: A:F.54, A:H.58 700.16: 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, Y.186, G.187, N.188, P.189 20 PLIP interactions: 6 interactions with chain D, 14 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, C:K.192, C:S.193, C:S.193, C:Y.227 pi-Stacking: D:F.54, D:H.58 Water bridges: C:R.61, C:R.61, C:R.61, C:S.193, C:S.193 pi-Cation interactions: C:R.61 700.23: 18 residues within 4Å: Chain C: T.39, V.41, F.54, H.58, Y.186, G.187, N.188, P.189 Chain D: R.61, L.64, V.65, W.68, P.189, W.190, E.191, K.192, S.193, P.230 17 PLIP interactions: 10 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:W.68, D:K.192, D:K.192, C:T.39, C:V.41, C:P.189 Hydrogen bonds: D:K.192, C:T.39 Water bridges: D:R.61, D:R.61, D:R.61, D:S.193, D:S.193, C:Y.186 pi-Cation interactions: D:R.61 pi-Stacking: C:F.54, C:H.58

4 x URC: URIC ACID(Non-covalent)

URC.4: 7 residues within 4Å: Chain A: N.283, D.284, F.286, E.383, A.611, G.613, Y.614 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.283, A:D.284, A:G.613 pi-Stacking: A:F.286, A:F.286, A:Y.614 URC.11: 5 residues within 4Å: Chain B: N.283, F.286, A.611, G.613, Y.614 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.283, B:G.613 pi-Stacking: B:F.286, B:F.286, B:Y.614 URC.17: 7 residues within 4Å: Chain C: N.283, D.284, F.286, E.383, A.611, G.613, Y.614 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.283, C:D.284, C:G.613 pi-Stacking: C:F.286, C:F.286, C:Y.614 URC.24: 5 residues within 4Å: Chain D: N.283, F.286, A.611, G.613, Y.614 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.283, D:G.613 pi-Stacking: D:F.286, D:F.286, D:Y.614

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

MRD.5: 7 residues within 4Å: Chain A: W.68, I.69, Q.72, R.194 Chain B: V.41, K.42, V.46 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.68, A:W.68, A:Q.72, B:K.42, B:V.46 Hydrogen bonds: A:R.194 Water bridges: A:W.68, A:R.194, A:R.194 MRD.6: 6 residues within 4Å: Chain A: I.171, R.172, D.173, G.174, Y.554, E.647 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.554 Hydrogen bonds: A:I.171, A:D.173, A:G.174 MRD.7: 4 residues within 4Å: Chain A: R.50, E.125, I.126, E.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.50, A:I.126 MRD.12: 7 residues within 4Å: Chain A: V.41, K.42, V.46 Chain B: W.68, Q.72, R.194 Ligands: MRD.13 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:V.41, B:R.194 Hydrophobic interactions: B:W.68, B:W.68, B:Q.72, B:Q.72 Water bridges: B:D.228, B:T.241 MRD.13: 5 residues within 4Å: Chain A: V.46 Chain B: R.194, F.197, R.243 Ligands: MRD.12 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.197, B:F.197 Hydrogen bonds: B:R.194, B:R.194 Water bridges: A:K.42 MRD.18: 7 residues within 4Å: Chain C: W.68, I.69, Q.72, R.194 Chain D: V.41, K.42, V.46 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain C Hydrophobic interactions: D:K.42, D:V.46, C:W.68, C:W.68, C:Q.72 Hydrogen bonds: C:R.194 Water bridges: C:W.68, C:R.194, C:R.194 MRD.19: 6 residues within 4Å: Chain C: I.171, R.172, D.173, G.174, Y.554, E.647 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.554 Hydrogen bonds: C:I.171, C:D.173, C:G.174 MRD.20: 4 residues within 4Å: Chain C: R.50, E.125, I.126, E.128 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Water bridges: A:G.527, A:G.527, C:R.50 Hydrogen bonds: C:R.50, C:I.126 MRD.25: 7 residues within 4Å: Chain C: V.41, K.42, V.46 Chain D: W.68, Q.72, R.194 Ligands: MRD.26 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:V.41, D:R.194 Hydrophobic interactions: D:W.68, D:W.68, D:Q.72, D:Q.72 Water bridges: D:D.228, D:T.241 MRD.26: 5 residues within 4Å: Chain C: V.46 Chain D: R.194, F.197, R.243 Ligands: MRD.25 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Water bridges: C:K.42 Hydrophobic interactions: D:F.197, D:F.197 Hydrogen bonds: D:R.194, D:R.194

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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