SMTL ID : 2ske.1

PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHITE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-dimer

Ligands

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 12 residues within 4Å: Chain A: G.135, L.136, L.139, N.284, H.377, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.135, A:L.136, A:N.284, A:N.284, A:Y.573, A:E.672, A:E.672, A:S.674, A:S.674, A:G.675 Water bridges: A:D.283, A:K.574, A:A.673 GLC.5: 12 residues within 4Å: Chain B: G.135, L.136, L.139, N.284, H.377, V.455, N.484, Y.573, E.672, A.673, S.674, G.675 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.135, B:L.136, B:N.284, B:N.284, B:H.377, B:E.672, B:S.674, B:S.674, B:G.675 Water bridges: B:D.283, B:K.574, B:A.673

2 x PO3: PHOSPHITE ION(Non-covalent)

PO3.2: 7 residues within 4Å: Chain A: K.568, K.574, E.672, G.675, T.676, G.677 Ligands: PLP.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:T.676, A:G.677 Water bridges: A:G.135, A:K.568, A:K.574, A:K.574, A:K.574, A:G.675, A:N.678 Salt bridges: A:K.568, A:K.574 PO3.6: 7 residues within 4Å: Chain B: K.568, K.574, E.672, G.675, T.676, G.677 Ligands: PLP.7 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:T.676, B:G.677 Water bridges: B:G.135, B:K.568, B:K.574, B:K.574, B:K.574, B:G.675, B:N.678 Salt bridges: B:K.568, B:K.574

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

PLP.3: 13 residues within 4Å: Chain A: Y.90, G.134, G.135, R.138, W.491, Y.648, R.649, V.650, A.653, T.676, G.677, K.680 Ligands: PO3.2 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.138, A:Y.648, A:K.680 Hydrogen bonds: A:G.677 Water bridges: A:Y.90 PLP.7: 13 residues within 4Å: Chain B: Y.90, G.134, G.135, R.138, W.491, Y.648, R.649, V.650, A.653, T.676, G.677, K.680 Ligands: PO3.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.138, B:Y.648, B:K.680 Hydrogen bonds: B:Y.648, B:G.677

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.4: 7 residues within 4Å: Chain A: Q.71, Q.72, Y.75, R.309, R.310 Chain B: D.42, V.45 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:D.42, A:Q.72 Salt bridges: A:R.309, A:R.310 pi-Stacking: A:Y.75, A:Y.75 IMP.8: 7 residues within 4Å: Chain A: D.42, V.45 Chain B: Q.71, Q.72, Y.75, R.309, R.310 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:D.42, B:Q.72 Salt bridges: B:R.309, B:R.310 pi-Stacking: B:Y.75, B:Y.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oikonomakos, N.G. et al., Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal. Protein Sci. (1996)

Release Date

1998-12-16

Peptides

PYRIDOXAL PHOSPHORYLASE B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PYRIDOXAL PHOSPHORYLASE B

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