SMTL ID : 3ahc.1

Resting form of Phosphoketolase from Bifidobacterium Breve

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:Y.237, H2O.18 MG.16: 4 residues within 4Å: Chain B: D.202, N.235, Y.237 Ligands: TPP.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.202, B:Y.237, H2O.52

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 25 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.1 21 PLIP interactions: 18 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.176, A:K.238, A:I.239, A:I.239, B:D.456 Hydrogen bonds: A:T.87, 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, 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.17: 25 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.16 19 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:E.176, B:K.238, B:I.239, B:I.239, A:D.456 Hydrogen bonds: 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 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.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.746 NA.18: 5 residues within 4Å: Chain A: H.746, D.747 Chain B: H.746, D.747 Ligands: NA.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.746

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

EDO.4: 6 residues within 4Å: Chain A: N.657, D.658, T.720, A.721, D.722, K.723 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: E.647, A.654, N.656, N.657, K.690 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: N.65, K.69, E.143 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: D.250, E.251, H.254 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: Q.147, K.148, R.151 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: A.541, R.544, E.545 Chain B: F.571, G.758, S.759 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: F.271, P.319, K.332, E.334, G.335 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain A: V.268, F.271 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: Y.775, L.797, F.800, E.817 Ligand excluded by PLIP EDO.13: 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 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: T.586, F.587, Q.701 Chain B: R.737 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain B: N.657, D.658, T.720, A.721, D.722, K.723 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: E.647, A.654, N.656, N.657, K.690 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: N.65, K.69, E.143 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: D.250, E.251, H.254 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: Q.147, K.148, R.151 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: F.571, G.758, S.759 Chain B: A.541, R.544, E.545 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain B: F.271, P.319, K.332, E.334, G.335 Ligand excluded by PLIP EDO.26: 2 residues within 4Å: Chain B: V.268, F.271 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: Y.775, L.797, F.800, E.817 Ligand excluded by PLIP EDO.28: 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 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: R.737 Chain B: T.586, F.587, Q.701 Ligand excluded by PLIP

2 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.15: 7 residues within 4Å: Chain A: Q.341 Chain B: E.430, R.462, D.567, H.568, K.625, P.627 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.341, B:R.462, B:R.462 Water bridges: B:R.565 2PE.30: 7 residues within 4Å: Chain A: E.430, R.462, D.567, H.568, K.625, P.627 Chain B: Q.341 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.462, A:R.462, A:H.568, B:Q.341 Water bridges: A:R.565

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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