SMTL ID : 3bd7.1

Glycogen Phosphorylase complex with 1(-D-glucopyranosyl) thymine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 residues within 4Å: Chain A: Y.90, G.134, G.135, R.138, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.90, A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:G.677 Water bridges: A:K.574, A:K.574, A:N.678, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.4: 16 residues within 4Å: Chain B: Y.90, G.134, G.135, R.138, W.491, V.567, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:Y.90, B:Y.648, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:T.676, B:G.677 Water bridges: B:K.574, B:K.574, B:N.678, B:N.678 Salt bridges: B:K.568, B:K.574

4 x CKB: 1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione(Non-covalent)

CKB.2: 6 residues within 4Å: Chain A: N.282, F.285, A.610, G.612, Y.613, H.614 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.285, A:A.610, A:Y.613 Hydrogen bonds: A:G.612, A:H.614 Water bridges: A:D.283, A:M.615 pi-Stacking: A:F.285, A:Y.613 CKB.3: 16 residues within 4Å: Chain A: G.135, L.136, L.139, D.283, N.284, D.339, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675, T.676 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.378 Hydrogen bonds: A:G.135, A:L.136, A:D.283, A:N.284, A:N.284, A:N.284, A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:E.88, A:G.137, A:A.673, A:T.676 CKB.5: 6 residues within 4Å: Chain B: N.282, F.285, A.610, G.612, Y.613, H.614 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.285, B:A.610, B:Y.613 Hydrogen bonds: B:G.612, B:H.614 Water bridges: B:D.283, B:M.615 pi-Stacking: B:F.285, B:Y.613 CKB.6: 16 residues within 4Å: Chain B: G.135, L.136, L.139, D.283, N.284, D.339, H.377, T.378, V.455, N.484, Y.573, E.672, A.673, S.674, G.675, T.676 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:T.378 Hydrogen bonds: B:G.135, B:L.136, B:D.283, B:N.284, B:N.284, B:N.284, B:H.377, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:G.137, B:Y.573, B:A.673, B:T.676

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cisma, C. et al., D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b. To be Published

Release Date

2008-11-18

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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