- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 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 PLIPEDO.5: 5 residues within 4Å:- Chain A: E.647, A.654, N.656, N.657, K.690
Ligand excluded by PLIPEDO.6: 2 residues within 4Å:- Chain A: N.65, K.69
Ligand excluded by PLIPEDO.7: 3 residues within 4Å:- Chain A: D.250, E.251, H.254
Ligand excluded by PLIPEDO.8: 3 residues within 4Å:- Chain A: Q.147, K.148, R.151
Ligand excluded by PLIPEDO.9: 5 residues within 4Å:- Chain A: R.544, E.545
- Chain B: F.571, G.758, S.759
Ligand excluded by PLIPEDO.10: 4 residues within 4Å:- Chain A: F.271, P.319, K.332, E.334
Ligand excluded by PLIPEDO.11: 3 residues within 4Å:- Chain A: V.268, F.271, R.317
Ligand excluded by PLIPEDO.12: 4 residues within 4Å:- Chain A: Y.775, L.797, F.800, E.817
Ligand excluded by PLIPEDO.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 PLIPEDO.14: 4 residues within 4Å:- Chain A: T.586, F.587, Q.701
- Chain B: R.737
Ligand excluded by PLIPEDO.18: 6 residues within 4Å:- Chain B: N.657, D.658, T.720, A.721, D.722, K.723
Ligand excluded by PLIPEDO.19: 5 residues within 4Å:- Chain B: E.647, A.654, N.656, N.657, K.690
Ligand excluded by PLIPEDO.20: 2 residues within 4Å:- Chain B: N.65, K.69
Ligand excluded by PLIPEDO.21: 3 residues within 4Å:- Chain B: D.250, E.251, H.254
Ligand excluded by PLIPEDO.22: 3 residues within 4Å:- Chain B: Q.147, K.148, R.151
Ligand excluded by PLIPEDO.23: 5 residues within 4Å:- Chain A: F.571, G.758, S.759
- Chain B: R.544, E.545
Ligand excluded by PLIPEDO.24: 4 residues within 4Å:- Chain B: F.271, P.319, K.332, E.334
Ligand excluded by PLIPEDO.25: 3 residues within 4Å:- Chain B: V.268, F.271, R.317
Ligand excluded by PLIPEDO.26: 4 residues within 4Å:- Chain B: Y.775, L.797, F.800, E.817
Ligand excluded by PLIPEDO.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 PLIPEDO.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
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 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)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 22 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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
AB
A