SMTL ID : 5iko.1

Crystal structure of human brain glycogen phosphorylase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

8 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.1: 5 residues within 4Å: Chain A: L.717, D.721, A.724, K.728, Y.735 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.728 P6G.2: 12 residues within 4Å: Chain A: W.71, I.72, Q.75, Q.76, Y.79, R.197, Y.200, D.231, T.244 Chain C: V.44, D.46, V.49 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.197, A:D.231 P6G.6: 5 residues within 4Å: Chain B: L.717, D.721, A.724, K.728, Y.735 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.728 P6G.7: 12 residues within 4Å: Chain B: W.71, I.72, Q.75, Q.76, Y.79, R.197, Y.200, D.231, T.244 Chain D: V.44, D.46, V.49 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.197, B:D.231 P6G.11: 5 residues within 4Å: Chain C: L.717, D.721, A.724, K.728, Y.735 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.728, C:Y.735 P6G.12: 12 residues within 4Å: Chain A: V.44, D.46, V.49 Chain C: W.71, I.72, Q.75, Q.76, Y.79, R.197, Y.200, D.231, T.244 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.197, C:D.231, C:D.231 P6G.16: 5 residues within 4Å: Chain D: L.717, D.721, A.724, K.728, Y.735 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.728, D:Y.735 P6G.17: 12 residues within 4Å: Chain B: V.44, D.46, V.49 Chain D: W.71, I.72, Q.75, Q.76, Y.79, R.197, Y.200, D.231, T.244 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.197, D:D.231, D:D.231

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

PO4.3: 5 residues within 4Å: Chain A: H.212, V.217, W.365, R.402 Ligands: PO4.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.212 Salt bridges: A:R.402 PO4.4: 4 residues within 4Å: Chain A: W.365, A.409, R.413 Ligands: PO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.365 Salt bridges: A:R.413 PO4.8: 5 residues within 4Å: Chain B: H.212, V.217, W.365, R.402 Ligands: PO4.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.212 Salt bridges: B:R.402 PO4.9: 4 residues within 4Å: Chain B: W.365, A.409, R.413 Ligands: PO4.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.365 Salt bridges: B:R.413 PO4.13: 5 residues within 4Å: Chain C: H.212, V.217, W.365, R.402 Ligands: PO4.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.212 Salt bridges: C:R.402 PO4.14: 4 residues within 4Å: Chain C: W.365, A.409, R.413 Ligands: PO4.13 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:W.365 Salt bridges: C:R.413 PO4.18: 5 residues within 4Å: Chain D: H.212, V.217, W.365, R.402 Ligands: PO4.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:H.212 Salt bridges: D:R.402 PO4.19: 4 residues within 4Å: Chain D: W.365, A.409, R.413 Ligands: PO4.18 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:W.365 Salt bridges: D:R.413

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

PLP.5: 14 residues within 4Å: Chain A: Y.94, G.139, R.142, W.495, K.572, Y.652, R.653, V.654, A.657, G.679, T.680, G.681, N.682, K.684 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.94, A:R.142, A:Y.652, A:K.684 Hydrogen bonds: A:T.680, A:G.681, A:K.684 Salt bridges: A:K.572, A:K.578 PLP.10: 14 residues within 4Å: Chain B: Y.94, G.139, R.142, W.495, K.572, Y.652, R.653, V.654, A.657, G.679, T.680, G.681, N.682, K.684 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.94, B:R.142, B:Y.652, B:K.684 Hydrogen bonds: B:T.680, B:G.681, B:K.684 Salt bridges: B:K.572, B:K.578 PLP.15: 14 residues within 4Å: Chain C: Y.94, G.139, R.142, W.495, K.572, Y.652, R.653, V.654, A.657, G.679, T.680, G.681, N.682, K.684 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.94, C:R.142, C:Y.652, C:K.684 Hydrogen bonds: C:T.680, C:G.681 Salt bridges: C:K.572, C:K.578 PLP.20: 14 residues within 4Å: Chain D: Y.94, G.139, R.142, W.495, K.572, Y.652, R.653, V.654, A.657, G.679, T.680, G.681, N.682, K.684 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.94, D:R.142, D:Y.652, D:K.684 Hydrogen bonds: D:T.680, D:G.681 Salt bridges: D:K.572, D:K.578

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathieu, C. et al., Insights into Brain Glycogen Metabolism: THE STRUCTURE OF HUMAN BRAIN GLYCOGEN PHOSPHORYLASE. J.Biol.Chem. (2016)

Release Date

2016-07-20

Peptides

Glycogen phosphorylase, brain form: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Glycogen phosphorylase, brain form

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