SMTL ID : 3ahd.1

Phosphoketolase from Bifidobacterium Breve complexed with 2-acetyl-thiamine diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.202, N.235, Y.237 Ligands: HTL.2 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: HTL.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.202, B:Y.237, H2O.46

2 x HTL: 2-ACETYL-THIAMINE DIPHOSPHATE(Non-covalent)

HTL.2: 29 residues within 4Å: Chain A: H.84, T.87, P.115, H.117, H.162, 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, N.569, H.573 Ligands: MG.1 23 PLIP interactions: 19 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:H.117, A:E.176, A:K.238, A:I.239, A:I.239 Hydrogen bonds: A:T.87, A:G.175, A:L.177, A:D.202, A:G.203, A:E.204, A:N.235, B:E.457 Water bridges: A:T.87, A:N.235, B:E.499, B:N.569 Salt bridges: A:H.117, A:H.117, A:K.320, A:K.320, A:H.340 pi-Stacking: B:F.524 HTL.9: 29 residues within 4Å: Chain A: P.455, D.456, E.457, L.497, E.499, Y.521, F.524, N.569, H.573 Chain B: H.84, T.87, P.115, H.117, H.162, 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 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:H.117, B:E.176, B:K.238, B:I.239, B:I.239 Hydrogen bonds: B:G.175, B:L.177, B:D.202, B:G.203, B:E.204, B:N.235, A:N.569 Water bridges: B:T.87, B:N.235, A:Y.521 Salt bridges: B:H.117, B:H.117, B:K.320, B:K.320, B:H.340 pi-Stacking: A:F.524

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: H.746, D.747 Chain B: H.746, D.747 Ligands: NA.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.747 Water bridges: A:D.747 NA.10: 5 residues within 4Å: Chain A: H.746, D.747 Chain B: H.746, D.747 Ligands: NA.3 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.747 Water bridges: A:D.747

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: Y.775, L.797, F.800, E.817 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.817 EDO.5: 3 residues within 4Å: Chain A: Q.31, K.32, D.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.32 EDO.6: 9 residues within 4Å: Chain A: K.472, V.483, D.484, E.485, M.487 Chain B: A.240, N.241, P.242, W.337 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.472, A:E.485 Water bridges: A:V.483, A:D.484 EDO.7: 4 residues within 4Å: Chain A: F.271, P.319, K.332, E.334 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.332, A:E.334 EDO.11: 4 residues within 4Å: Chain B: Y.775, L.797, F.800, E.817 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.817 EDO.12: 3 residues within 4Å: Chain B: Q.31, K.32, D.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.32 EDO.13: 9 residues within 4Å: Chain A: A.240, N.241, P.242, W.337 Chain B: K.472, V.483, D.484, E.485, M.487 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.472, B:E.485 Water bridges: B:D.484, B:D.484 EDO.14: 4 residues within 4Å: Chain B: F.271, P.319, K.332, E.334 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.332, B:E.334, B:E.334

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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