SMTL ID : 2r5n.1

Crystal structure of transketolase from Escherichia coli in noncovalent complex with acceptor aldose ribose 5-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

1 x R5P: RIBOSE-5-PHOSPHATE(Non-covalent)

R5P.1: 13 residues within 4Å: Chain A: R.358, S.385, F.434, H.461, D.469, H.473, R.520 Chain B: H.26, I.189, H.261, G.262 Ligands: RP5.13, TPP.14 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.385, A:S.385, B:H.261, B:H.261 Water bridges: A:R.358, A:R.358, B:R.91 Salt bridges: A:R.358, A:H.461, A:R.520

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: TPP.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.1 CA.12: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.33

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.3: 23 residues within 4Å: Chain A: A.29, H.66, G.114, P.115, L.116, G.154, D.155, G.156, E.160, N.185, I.187, S.188, I.189, I.247, H.261 Chain B: D.381, V.409, E.411, F.437, Y.440, H.473 Ligands: CA.2, RP5.23 17 PLIP interactions: 14 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.116, A:I.189, B:F.437, B:Y.440 Hydrogen bonds: A:G.114, A:L.116, A:D.155, A:G.156, A:N.185 Water bridges: A:A.29, A:N.64, A:N.64, A:G.154 Salt bridges: A:H.66, A:H.66, A:H.261 pi-Stacking: B:F.437 TPP.14: 25 residues within 4Å: Chain A: D.381, L.382, V.409, E.411, F.437, Y.440, H.473 Chain B: A.29, H.66, G.114, P.115, L.116, G.154, D.155, G.156, E.160, N.185, I.187, S.188, I.189, I.247, H.261 Ligands: R5P.1, CA.12, RP5.13 18 PLIP interactions: 4 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:L.382, A:F.437, A:Y.440, B:L.116, B:I.189 pi-Stacking: A:F.437 Hydrogen bonds: B:G.114, B:L.116, B:D.155, B:G.156, B:N.185 Water bridges: B:A.29, B:N.64, B:N.64, B:G.154 Salt bridges: B:H.66, B:H.66, B:H.261

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

EDO.4: 5 residues within 4Å: Chain A: Y.505, R.509, D.511, K.591 Ligands: EDO.5 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.505, E.508, R.509 Ligands: EDO.4 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: P.52, R.57, V.103, A.107, G.108, V.109, E.110 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: R.274, E.275, W.279, K.280 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: E.6, G.278, W.279, K.280, Y.281 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: K.131, T.172, L.173, K.174, I.396, N.397 Ligand excluded by PLIP EDO.10: 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.11: 5 residues within 4Å: Chain A: S.559, E.560, L.563, F.645, F.650 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: R.483, V.484 Chain B: I.615, D.617, T.633 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: P.52, R.57, V.103, T.106, G.108, V.109 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain B: I.345, V.501, K.504, L.533, A.534, I.536, A.537 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain B: A.353, K.354 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: S.559, E.560, F.645, F.650 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: R.4, R.42 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: F.635 Chain B: A.449, L.450, K.452, N.487 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: G.186, H.192, V.193, E.194 Ligand excluded by PLIP

2 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)

RP5.13: 11 residues within 4Å: Chain A: R.358, S.385, H.461, D.469, R.520 Chain B: H.26, I.189, H.261, G.262 Ligands: R5P.1, TPP.14 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.385, A:S.385, B:H.261 Water bridges: A:R.358, A:R.358, B:G.262 Salt bridges: A:R.358, A:H.461, A:R.520, B:H.261 RP5.23: 10 residues within 4Å: Chain A: H.26, I.189, H.261, G.262 Chain B: R.358, S.385, H.461, D.469, R.520 Ligands: TPP.3 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.385, B:S.385, A:H.261 Water bridges: B:R.358, B:R.358, B:R.358, B:P.384, B:S.385, B:H.461, B:R.520, B:R.520, A:R.91 Salt bridges: B:R.358, B:H.461, B:R.520

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Asztalos, P. et al., Strain and Near Attack Conformers in Enzymic Thiamin Catalysis: X-ray Crystallographic Snapshots of Bacterial Transketolase in Covalent Complex with Donor Ketoses Xylulose 5-phosphate and Fructose 6-phosphate, and in Noncovalent Complex with Acceptor Aldose Ribose 5-phosphate. Biochemistry (2007)

Release Date

2007-11-06

Peptides

Transketolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase 1

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