SMTL ID : 3ahf.1

Phosphoketolase from Bifidobacterium Breve complexed with inorganic phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 26 residues within 4Å: Chain A: T.87, P.115, H.117, G.175, E.176, L.177, G.201, D.202, G.203, E.204, H.233, N.235, Y.237, K.238, I.239, K.320, H.340 Chain B: P.455, D.456, E.457, L.497, E.499, Y.521, F.524 Ligands: MG.2, PO4.3 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:E.176, A:K.238, A:I.239, A:I.239, B:D.456, B:L.497, B:L.497 Hydrogen bonds: A:T.87, A:G.175, A:L.177, A:D.202, A:G.203, A:E.204, A:N.235 Water bridges: A:N.235, A:K.320, B:E.499 Salt bridges: A:H.117, A:H.117, A:K.320, A:K.320, A:H.340 pi-Stacking: B:F.524 TPP.7: 26 residues within 4Å: Chain A: P.455, D.456, E.457, L.497, E.499, Y.521, F.524 Chain B: T.87, P.115, H.117, G.175, E.176, L.177, G.201, D.202, G.203, E.204, H.233, N.235, Y.237, K.238, I.239, K.320, H.340 Ligands: MG.8, PO4.9 23 PLIP interactions: 19 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.176, B:K.238, B:I.239, B:I.239, A:D.456, A:L.497, A:L.497 Hydrogen bonds: B:T.87, B:T.87, B:G.175, B:L.177, B:D.202, B:G.203, B:E.204, B:N.235 Water bridges: B:N.235, B:K.320 Salt bridges: B:H.117, B:H.117, B:K.320, B:K.320, B:H.340 pi-Stacking: A:F.524

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.202, N.235, Y.237 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:Y.237, H2O.17 MG.8: 4 residues within 4Å: Chain B: D.202, N.235, Y.237 Ligands: TPP.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.202, B:Y.237, H2O.37

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

PO4.3: 8 residues within 4Å: Chain A: H.84, I.239, H.340, Q.341 Chain B: Y.521, H.568, N.569 Ligands: TPP.1 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.341, B:Y.521, B:N.569 Salt bridges: A:H.84, A:H.340 Water bridges: B:H.568 PO4.9: 8 residues within 4Å: Chain A: Y.521, H.568, N.569 Chain B: H.84, I.239, H.340, Q.341 Ligands: TPP.7 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.521, A:Y.521, A:N.569, B:Q.341 Water bridges: A:H.568 Salt bridges: B:H.84, B:H.340

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: A.240, N.241 Chain B: D.456, E.457, T.458, A.459, Y.467, K.472, E.495 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.459, B:K.472, B:E.495 Water bridges: B:S.460 GOL.5: 2 residues within 4Å: Chain A: N.273, D.275 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.275 GOL.6: 7 residues within 4Å: Chain A: D.771, A.776, A.779, K.783, I.794, N.798, R.801 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.776 Water bridges: A:R.801 GOL.10: 9 residues within 4Å: Chain A: D.456, E.457, T.458, A.459, Y.467, K.472, E.495 Chain B: A.240, N.241 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.459, A:Y.467, A:K.472, A:E.495 Water bridges: A:S.460 GOL.11: 2 residues within 4Å: Chain B: N.273, D.275 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.275 Water bridges: B:D.275 GOL.12: 7 residues within 4Å: Chain B: D.771, A.776, A.779, K.783, I.794, N.798, R.801 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.776 Water bridges: B:R.801

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, R. et al., Crystal Structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism. J.Biol.Chem. (2010)

Release Date

2010-08-25

Peptides

Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Xylulose 5-phosphate/fructose 6-phosphate phosphoketolase

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