SMTL ID : 2r8o.1

Transketolase from E. coli in complex with substrate D-xylulose-5-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.47 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: T5X.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.1 CA.4: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: T5X.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.25

2 x T5X: 2-C-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thia zol-3-ium-2-yl}-5-O-phosphono-D-xylitol(Non-covalent)

T5X.2: 29 residues within 4Å: Chain A: H.26, A.29, H.66, H.100, 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, S.385, V.409, E.411, F.434, F.437, Y.440, H.461, D.469, H.473, R.520 Ligands: CA.1 32 PLIP interactions: 22 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:L.116, A:I.189, A:I.189, B:D.381, 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:E.160, A:N.185, A:H.261 Water bridges: A:A.29, A:H.66, A:H.66, A:G.154, A:C.157, A:D.183, A:D.183, A:D.183, B:R.358, B:E.411, B:R.520 Salt bridges: A:H.66, A:H.66, A:H.261, B:H.461, B:R.520 pi-Stacking: B:F.437 T5X.5: 29 residues within 4Å: Chain A: D.381, S.385, V.409, E.411, F.434, F.437, Y.440, H.461, D.469, H.473, R.520 Chain B: H.26, A.29, H.66, H.100, 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: CA.4 36 PLIP interactions: 23 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:L.116, B:L.116, B:I.189, B:I.189, 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:E.160, B:N.185, B:H.261, A:S.385, A:D.469 Water bridges: B:A.29, B:H.66, B:H.66, B:G.154, B:C.157, B:D.183, B:D.183, B:D.183, A:R.358, A:R.358, A:E.411, A:D.469, A:R.520 Salt bridges: B:H.66, B:H.66, B:H.261, A:H.461, A:R.520 pi-Stacking: A:F.437

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

EDO.3: 6 residues within 4Å: Chain A: I.615, D.617, T.633 Chain B: R.483, V.484, K.621 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:T.633, B:K.621 Water bridges: B:K.621, B:K.621 EDO.6: 5 residues within 4Å: Chain B: E.6, G.278, W.279, K.280, Y.281 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.6, B:K.280 EDO.7: 4 residues within 4Å: Chain B: Y.505, E.508, R.509 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.505 Water bridges: B:E.508 EDO.8: 2 residues within 4Å: Chain B: R.538, Q.592 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.538, B:Q.592 EDO.9: 5 residues within 4Å: Chain B: Y.505, R.509, D.511, K.591 Ligands: EDO.7 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.509, B:R.509, B:K.591 EDO.10: 7 residues within 4Å: Chain B: F.375, T.388, W.390, S.393, N.403, Y.404, Y.430 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.393, B:Y.430 EDO.11: 5 residues within 4Å: Chain B: P.52, V.103, A.107, G.108, V.109 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.106, B:G.108 Water bridges: B:G.104, B:V.109, B:E.110, B:L.423 EDO.12: 4 residues within 4Å: Chain B: S.559, E.560, F.645, F.650 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.560, B:E.560 EDO.13: 6 residues within 4Å: Chain B: K.131, T.172, L.173, K.174, I.396, N.397 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.131, B:I.396 EDO.14: 9 residues within 4Å: Chain B: L.435, D.462, P.475, V.476, V.479, R.492, I.517, A.613, G.614 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.613 Water bridges: B:V.479 EDO.15: 5 residues within 4Å: Chain B: A.55, W.307, F.311, F.325, T.326 No protein-ligand interaction detected (PLIP)

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

2007-12-11

Peptides

Transketolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase 1

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