SMTL ID : 3ahi.1

H320A mutant of Phosphoketolase from Bifidobacterium Breve complexed with acetyl thiamine diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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.15 MG.14: 4 residues within 4Å: Chain B: D.202, N.235, Y.237 Ligands: HTL.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.202, B:Y.237, H2O.40

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

HTL.2: 27 residues within 4Å: Chain A: H.84, 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 Chain B: P.455, D.456, E.457, L.497, E.499, Y.521, F.524, N.569, H.573 Ligands: MG.1 25 PLIP interactions: 20 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:H.117, 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:N.235, B:E.457 Water bridges: A:T.87, A:N.235, A:N.235, A:K.320, A:K.320, B:E.499, B:N.569 Salt bridges: A:H.117, A:K.320, A:K.320 pi-Stacking: B:F.524 HTL.15: 27 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, 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 Ligands: MG.14 22 PLIP interactions: 4 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:D.456, B:H.117, B:E.176, B:K.238, B:I.239, B:I.239 Hydrogen bonds: A:N.569, B:G.175, B:L.177, B:D.202, B:G.203, B:E.204 Water bridges: A:Y.521, B:T.87, B:N.235, B:N.235, B:K.320, B:K.320 pi-Stacking: A:F.524 Salt bridges: B:H.117, B:K.320, B:K.320

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.16 No protein-ligand interaction detected (PLIP) NA.16: 5 residues within 4Å: Chain A: H.746, D.747 Chain B: H.746, D.747 Ligands: NA.3 No protein-ligand interaction detected (PLIP)

20 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: D.250, E.251, H.254 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: Q.147, K.148, R.151 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: R.544, E.545 Chain B: F.571, G.758 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: G.270, F.271, K.332, E.334, G.335 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: V.268, F.271, R.317 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: Y.775, L.797, F.800, E.817 Ligand excluded by PLIP EDO.12: 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.13: 4 residues within 4Å: Chain A: T.586, F.587, Q.701 Chain B: R.737 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: N.657, D.658, T.720, A.721, D.722, K.723 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: E.647, A.654, N.656, N.657, K.690 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: D.250, E.251, H.254 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: Q.147, K.148, R.151 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: F.571, G.758 Chain B: R.544, E.545 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: G.270, F.271, K.332, E.334, G.335 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain B: V.268, F.271, R.317 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: Y.775, L.797, F.800, E.817 Ligand excluded by PLIP EDO.25: 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.26: 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