SMTL ID : 8wa7.1

E.coli transketolase soaked with donor ketose D-fructose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: L.45, K.46, H.47, A.296, A.299, G.300, K.303 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: S.559, E.560, L.563, F.645, F.650 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: I.615, D.617, T.633 Chain B: R.483, V.484 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: L.45, H.47, R.57, D.58, R.59, F.60, E.110 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: H.26, I.189, H.261 Chain B: F.434, D.469 Ligands: THD.13 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: F.375, T.388, W.390, S.393, N.403, Y.404, Y.430 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: A.55, W.307, F.311, T.326 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: Y.505, A.537, R.538, Q.592 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: E.102, V.103, T.112, L.450, M.451 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: Q.526, E.527, K.544 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: S.385 Chain B: H.261 Ligands: EDO.22 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain B: E.6, G.278, W.279, K.280, Y.281 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain B: Y.505, E.508, R.509 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: R.509, D.511, K.591 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: F.375, T.388, W.390, S.393, N.403, Y.404, Y.430 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain B: R.538, Q.592 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: S.559, E.560, F.645, F.650 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain B: K.21, K.88, Q.92 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: F.434, D.469 Chain B: H.26, I.189, H.261 Ligands: EDO.12, THD.27 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: A.55, W.307, F.311, F.325, T.326 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: L.45, K.46, H.47, A.296, A.299, G.300, K.303 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain B: L.45, H.47, R.57, D.58, R.59, F.60, E.110 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: Y.182, D.184, F.197, D.199, T.201 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: Q.136, F.137, R.139, E.321, R.328 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.136, A:R.139, A:E.321 Water bridges: A:R.139, A:R.139

2 x THD: 2-[3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-2-(1,2-DIHYDROXYETHYL)-4-METHYL-1,3-THIAZOL-3-IUM-5-YL]ETHYL TRIHYDROGEN DIPHOSPHATE(Non-covalent)

THD.13: 26 residues within 4Å: Chain A: H.26, A.29, H.66, H.100, G.114, P.115, L.116, D.155, G.156, E.160, N.185, I.187, S.188, I.189, I.247, H.261 Chain B: D.381, L.382, V.409, E.411, F.434, F.437, Y.440, H.473 Ligands: EDO.5, MG.14 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.116, A:I.189, A:I.189, B:V.409, B:F.437, B:Y.440 Hydrogen bonds: A:H.100, A:G.114, A:L.116, A:D.155, A:G.156, A:N.185 Water bridges: A:A.29, A:H.66, A:C.157 Salt bridges: A:H.66, A:H.66, A:H.261 pi-Stacking: B:F.437 THD.27: 26 residues within 4Å: Chain A: D.381, L.382, V.409, E.411, F.434, F.437, Y.440, H.473 Chain B: H.26, A.29, H.66, H.100, G.114, P.115, L.116, D.155, G.156, E.160, N.185, I.187, S.188, I.189, I.247, H.261 Ligands: EDO.22, MG.28 23 PLIP interactions: 18 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.189, A:L.382, A:V.409, A:F.437, A:Y.440 Hydrogen bonds: B:H.100, B:G.114, B:L.116, B:D.155, B:G.156, B:N.185 Water bridges: B:A.29, B:N.64, B:H.66, B:H.66, B:C.157, B:D.183, B:D.183, B:N.185 Salt bridges: B:H.66, B:H.66, B:H.261 pi-Stacking: A:F.437

2 x MG: MAGNESIUM ION(Non-covalent)

MG.14: 4 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: THD.13 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.5 MG.28: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: THD.27 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Z. et al., Multifaceted Role of the Substrate Phosphate Group in Transketolase Catalysis. Acs Catalysis (2024)

Release Date

2024-01-24

Peptides

Transketolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase 1

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