SMTL ID : 5gpb.1

COMPARISON OF THE BINDING OF GLUCOSE AND GLUCOSE-1-PHOSPHATE DERIVATIVES TO T-STATE GLYCOGEN PHOSPHORYLASE B

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x GLC- GLC- GLC- GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose

GLC-GLC-GLC-GLC-GLC.1: 12 residues within 4Å: Chain A: Y.404, E.405, N.407, Q.408, L.411, V.422, L.425, R.426, S.429, V.431, E.433, K.437 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.408 GLC-GLC-GLC-GLC-GLC.5: 12 residues within 4Å: Chain B: Y.404, E.405, N.407, Q.408, L.411, V.422, L.425, R.426, S.429, V.431, E.433, K.437 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.408

4 x GPM: (1S)-1,5-anhydro-1-(phosphonomethyl)-D-glucitol(Non-covalent)

GPM.2: 16 residues within 4Å: Chain A: G.134, G.135, L.136, L.139, N.284, H.377, V.455, N.484, Y.573, K.574, E.672, A.673, S.674, G.675, T.676 Ligands: PLP.4 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.135, A:N.284, A:N.484, A:Y.573, A:K.574, A:E.672, A:E.672, A:A.673, A:S.674, A:S.674, A:G.675 Water bridges: A:K.574, A:T.676 GPM.3: 8 residues within 4Å: Chain A: Q.71, R.193, F.196, R.242, R.309, R.310 Chain B: V.40, V.45 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.193, A:R.193, A:R.242, A:R.242, A:R.309, A:R.309, A:R.310 GPM.6: 16 residues within 4Å: Chain B: G.134, G.135, L.136, L.139, N.284, H.377, V.455, N.484, Y.573, K.574, E.672, A.673, S.674, G.675, T.676 Ligands: PLP.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.135, B:N.284, B:H.377, B:N.484, B:Y.573, B:K.574, B:E.672, B:A.673, B:S.674, B:S.674, B:G.675 Water bridges: B:K.574, B:T.676 GPM.7: 8 residues within 4Å: Chain A: V.40, V.45 Chain B: Q.71, R.193, F.196, R.242, R.309, R.310 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.193, B:R.193, B:R.242, B:R.242, B:R.309, B:R.309, B:R.310

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

PLP.4: 16 residues within 4Å: Chain A: G.134, G.135, R.138, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, E.672, G.675, T.676, G.677, K.680 Ligands: GPM.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.138, A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:G.677 Water bridges: A:K.568, A:K.568, A:K.574, A:K.574, A:Q.665, A:N.678 Salt bridges: A:K.568, A:K.574 PLP.8: 16 residues within 4Å: Chain B: G.134, G.135, R.138, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, E.672, G.675, T.676, G.677, K.680 Ligands: GPM.6 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:R.138, B:Y.648, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:G.677 Water bridges: B:K.568, B:K.568, B:K.574, B:K.574, B:Q.665, B:N.678 Salt bridges: B:K.568, B:K.574

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin, J.L. et al., Comparison of the binding of glucose and glucose 1-phosphate derivatives to T-state glycogen phosphorylase b. Biochemistry (1990)

Release Date

1992-10-15

Peptides

GLYCOGEN PHOSPHORYLASE B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYCOGEN PHOSPHORYLASE B

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