SMTL ID : 1noj.1

COMPLEX OF GLYCOGEN PHOSPHORYLASE WITH A TRANSITION STATE ANALOGUE NOJIRIMYCIN TETRAZOLE AND PHOSPHATE IN THE T STATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 9 residues within 4Å: Chain A: G.134, G.135, L.136, R.569, Y.573, K.574, E.672 Ligands: PLP.3, NTZ.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.135, A:L.136, A:E.672 Water bridges: A:R.569, A:R.569 Salt bridges: A:R.569, A:K.574 PO4.2: 4 residues within 4Å: Chain A: Y.75, R.242, R.309, R.310 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.75, A:Y.75, A:Y.75, A:R.242, A:R.242 Water bridges: A:R.310, A:R.310 Salt bridges: A:R.309, A:R.310 PO4.5: 9 residues within 4Å: Chain B: G.134, G.135, L.136, R.569, Y.573, K.574, E.672 Ligands: PLP.7, NTZ.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.135, B:L.136, B:Y.573, B:E.672 Water bridges: B:R.569, B:R.569 Salt bridges: B:R.569, B:K.574 PO4.6: 4 residues within 4Å: Chain B: Y.75, R.242, R.309, R.310 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.75, B:Y.75, B:R.242, B:R.242 Water bridges: B:R.310, B:R.310 Salt bridges: B:R.309, B:R.310

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

PLP.3: 14 residues within 4Å: Chain A: G.134, G.135, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 Ligands: PO4.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.648, A:K.680 Hydrogen bonds: A:T.676, A:T.676, A:G.677 Water bridges: A:K.568, A:K.568, A:K.568, A:K.574 Salt bridges: A:K.568, A:K.574 PLP.7: 14 residues within 4Å: Chain B: G.134, G.135, W.491, K.568, K.574, Y.648, R.649, V.650, A.653, G.675, T.676, G.677, K.680 Ligands: PO4.5 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.648, B:K.680 Hydrogen bonds: B:Y.648, B:T.676, B:T.676, B:G.677 Water bridges: B:K.568, B:K.568, B:K.568, B:K.574 Salt bridges: B:K.568, B:K.574

2 x NTZ: NOJIRIMYCINE TETRAZOLE(Non-covalent)

NTZ.4: 13 residues within 4Å: Chain A: G.135, L.136, N.284, H.377, V.455, N.484, R.569, Y.573, E.672, A.673, S.674, G.675 Ligands: PO4.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.284, A:N.484, A:E.672, A:E.672, A:A.673, A:S.674, A:G.675, A:G.675 Water bridges: A:T.378, A:T.676 NTZ.8: 13 residues within 4Å: Chain B: G.135, L.136, N.284, H.377, V.455, N.484, R.569, Y.573, E.672, A.673, S.674, G.675 Ligands: PO4.5 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:N.284, B:H.377, B:N.484, B:E.672, B:A.673, B:S.674, B:G.675, B:G.675 Water bridges: B:T.676

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitchell, E.P. et al., Ternary complex crystal structures of glycogen phosphorylase with the transition state analogue nojirimycin tetrazole and phosphate in the T and R states. Biochemistry (1996)

Release Date

1996-07-11

Peptides

GLYCOGEN PHOSPHORYLASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GLYCOGEN PHOSPHORYLASE

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