SMTL ID : 2pyd.1 (1 other biounit)

The crystal structure of Glycogen phosphorylase in complex with glucose at 100 K

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 12 residues within 4Å: Chain A: G.136, L.137, L.140, N.285, H.378, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.136, A:L.137, A:N.285, A:N.285, A:N.485, A:E.673, A:E.673, A:A.674, A:S.675, A:G.676, A:G.676 Water bridges: A:D.284, A:D.284, A:Y.574, A:T.677 Salt bridges: A:H.378 GLC.20: 12 residues within 4Å: Chain B: G.136, L.137, L.140, N.285, H.378, V.456, N.485, Y.574, E.673, A.674, S.675, G.676 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:G.136, B:L.137, B:N.285, B:N.285, B:H.378, B:N.485, B:Y.574, B:E.673, B:A.674, B:S.675, B:G.676, B:G.676 Water bridges: B:D.284, B:D.284, B:Y.574, B:T.677 Salt bridges: B:H.378

36 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: W.68, I.69, Q.72, R.194 Chain B: V.41 Ligand excluded by PLIP DMS.3: 3 residues within 4Å: Chain A: D.62, H.63 Chain B: F.38 Ligand excluded by PLIP DMS.4: 6 residues within 4Å: Chain A: F.203, Q.220, V.222, A.273, K.295 Ligands: DMS.19 Ligand excluded by PLIP DMS.5: 4 residues within 4Å: Chain A: H.202, W.216, R.352, L.357 Ligand excluded by PLIP DMS.6: 6 residues within 4Å: Chain A: R.520, E.702, E.703, A.704, G.705, T.808 Ligand excluded by PLIP DMS.7: 5 residues within 4Å: Chain A: E.707, F.709, F.710, R.787, M.801 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: R.67, N.102, L.103, R.235, N.237, R.834 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain A: Y.549, E.553, Y.554, R.650 Ligand excluded by PLIP DMS.10: 8 residues within 4Å: Chain A: Q.265, L.268, D.269, N.271, L.272 Chain B: N.271, N.275 Ligands: DMS.29 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: L.550, Y.554, F.645, L.646, E.647 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: Y.727, H.768, D.770, R.771 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: I.532, A.536, P.795, R.796, T.799 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: P.195 Chain B: L.184, R.185, Y.186, G.187 Ligand excluded by PLIP DMS.15: 7 residues within 4Å: Chain A: R.428, T.467, I.468, F.469, K.470, D.471, F.472 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: I.264, Q.265 Chain B: Y.281, K.290, L.292 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: Q.409, L.412, N.413, A.416, L.426 Ligand excluded by PLIP DMS.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.19: 6 residues within 4Å: Chain A: L.272, N.275, L.292, K.295 Chain B: L.268 Ligands: DMS.4 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: V.41 Chain B: W.68, I.69, Q.72, R.194 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain A: F.38 Chain B: D.62, H.63 Ligand excluded by PLIP DMS.23: 6 residues within 4Å: Chain B: F.203, Q.220, V.222, A.273, K.295 Ligands: DMS.38 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain B: H.202, W.216, R.352, L.357 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain B: R.520, E.702, E.703, A.704, G.705, T.808 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain B: E.707, F.709, F.710, R.787, M.801 Ligand excluded by PLIP DMS.27: 6 residues within 4Å: Chain B: R.67, N.102, L.103, R.235, N.237, R.834 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain B: Y.549, E.553, Y.554, R.650 Ligand excluded by PLIP DMS.29: 8 residues within 4Å: Chain A: N.271, N.275 Chain B: Q.265, L.268, D.269, N.271, L.272 Ligands: DMS.10 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain B: L.550, Y.554, F.645, L.646, E.647 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain B: Y.727, H.768, D.770, R.771 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain B: I.532, A.536, P.795, R.796, T.799 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain A: L.184, R.185, Y.186, G.187 Chain B: P.195 Ligand excluded by PLIP DMS.34: 7 residues within 4Å: Chain B: R.428, T.467, I.468, F.469, K.470, D.471, F.472 Ligand excluded by PLIP DMS.35: 5 residues within 4Å: Chain A: Y.281, K.290, L.292 Chain B: I.264, Q.265 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: Q.409, L.412, N.413, A.416, L.426 Ligand excluded by PLIP DMS.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.38: 6 residues within 4Å: Chain A: L.268 Chain B: L.272, N.275, L.292, K.295 Ligands: DMS.23 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alexacou, K.M. et al., Crystallographic and computational studies on 4-phenyl-N-(beta-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: Comparison with alpha-D-glucose, N-acetyl-beta-D-glucopyranosylamine and N-benzoyl-N'-beta-D-glucopyranosyl urea binding. Proteins (2007)

Release Date

2008-04-01

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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