SMTL ID : 3ahg.1

H64A mutant of Phosphoketolase from Bifidobacterium Breve complexed with a tricyclic ring form of thiamine diphosphate

Coordinates

PDB Format Compare

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: HTD.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.202, A:Y.237, H2O.16 MG.15: 4 residues within 4Å: Chain B: D.202, N.235, Y.237 Ligands: HTD.16 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.202, B:Y.237, H2O.47

2 x HTD: 2-[(9aR)-2,7-dimethyl-9a,10-dihydro-5H-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-8-yl]ethyl trihydrogen diphosphate(Non-covalent)

HTD.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:G.175, A:L.177, A:D.202, A:G.203, A:E.204, A:H.233, A:N.235 Water bridges: A:T.87, 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 HTD.16: 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.15 19 PLIP interactions: 2 interactions with chain A, 17 interactions with chain B Hydrophobic interactions: A:D.456, B:E.176, B:K.238, B:I.239, B:I.239 pi-Stacking: A:F.524 Hydrogen bonds: B:G.175, B:L.177, B:D.202, B:G.203, B:E.204, B:H.233, B:N.235 Water bridges: B:T.87 Salt bridges: B:H.117, B:H.117, B:K.320, B:K.320, B:H.340

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.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.746 Water bridges: A:D.747 NA.17: 5 residues within 4Å: Chain A: H.746, D.747 Chain B: H.746, D.747 Ligands: NA.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.747 Water bridges: A:D.747

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: 2 residues within 4Å: Chain A: N.65, K.69 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: 5 residues within 4Å: Chain A: R.544, E.545 Chain B: F.571, G.758, S.759 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: F.271, P.319, K.332, E.334 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: V.268, F.271, R.317 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.18: 6 residues within 4Å: Chain B: N.657, D.658, T.720, A.721, D.722, K.723 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: E.647, A.654, N.656, N.657, K.690 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: N.65, K.69 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: D.250, E.251, H.254 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: Q.147, K.148, R.151 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: F.571, G.758, S.759 Chain B: R.544, E.545 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: F.271, P.319, K.332, E.334 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: V.268, F.271, R.317 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain B: Y.775, L.797, F.800, E.817 Ligand excluded by PLIP EDO.27: 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.28: 4 residues within 4Å: Chain A: R.737 Chain B: T.586, F.587, Q.701 Ligand excluded by PLIP

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