SMTL ID : 7q5i.1

A glucose-based molecular rotor probes the catalytic site of glycogen phosphorylase.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x I0F: 2-cyano-3-[4-(dimethylamino)phenyl]-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]propanamide(Non-covalent)

I0F.1: 27 residues within 4Å: Chain A: E.89, N.134, G.136, L.137, L.140, Y.281, N.283, D.284, F.286, F.287, E.288, R.293, H.342, H.378, T.379, A.384, E.386, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677, K.681 Ligands: CO3.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.137, A:D.284 Hydrogen bonds: A:G.136, A:L.137, A:H.378, A:H.378, A:H.378, A:N.485, A:E.673, A:A.674, A:S.675, A:G.676 Water bridges: A:G.138, A:H.378, A:K.575, A:E.673, A:T.677 pi-Cation interactions: A:H.342 I0F.6: 27 residues within 4Å: Chain B: E.89, N.134, G.136, L.137, L.140, Y.281, N.283, D.284, F.286, F.287, E.288, R.293, H.342, H.378, T.379, A.384, E.386, V.456, N.485, Y.574, E.673, A.674, S.675, G.676, T.677, K.681 Ligands: CO3.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.137, B:D.284 Hydrogen bonds: B:G.136, B:L.137, B:H.378, B:H.378, B:H.378, B:N.485, B:A.674, B:S.675, B:G.676 Water bridges: B:G.138, B:H.378, B:K.575, B:E.673, B:T.677 pi-Cation interactions: B:H.342

6 x CO3: CARBONATE ION(Non-functional Binders)

CO3.2: 5 residues within 4Å: Chain A: H.202, W.216, T.219, R.352, L.357 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.216, A:R.352 Water bridges: A:W.216 CO3.3: 7 residues within 4Å: Chain A: E.706, E.707, F.709, F.710, R.787, M.801 Ligands: BME.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.787, A:R.787 CO3.4: 8 residues within 4Å: Chain A: N.283, F.287, E.288, G.289, K.290, R.293, W.388 Ligands: I0F.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.283, A:N.283, A:E.288, A:R.293 CO3.7: 5 residues within 4Å: Chain B: H.202, W.216, T.219, R.352, L.357 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.216, B:R.352 Water bridges: B:W.216 CO3.8: 7 residues within 4Å: Chain B: E.706, E.707, F.709, F.710, R.787, M.801 Ligands: BME.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.787, B:R.787 CO3.9: 8 residues within 4Å: Chain B: N.283, F.287, E.288, G.289, K.290, R.293, W.388 Ligands: I0F.6 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.283, B:N.283, B:E.288, B:R.293

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.5: 7 residues within 4Å: Chain A: F.709, F.710, I.711, F.712, C.784, R.787 Ligands: CO3.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.709, A:I.711 BME.10: 7 residues within 4Å: Chain B: F.709, F.710, I.711, F.712, C.784, R.787 Ligands: CO3.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.709, B:I.711

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minadakis, M.P. et al., A glucose-based molecular rotor inhibitor of glycogen phosphorylase as a probe of cellular enzymatic function. Org.Biomol.Chem. (2022)

Release Date

2022-03-02

Peptides

Glycogen phosphorylase, muscle form: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
AAA

Glycogen phosphorylase, muscle form

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