SMTL ID : 5hht.1

Crystal structure of E. coli transketolase triple variant Ser385Tyr/Asp469Thr/Arg520Gln

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 5 residues within 4Å: Chain A: I.615, D.617, T.633 Chain B: R.483, V.484 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: L.389, S.393, K.394, A.395, E.398, H.406 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: S.559, E.560, L.563, F.645, F.650 Ligand excluded by PLIP EDO.6: 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.7: 5 residues within 4Å: Chain A: A.55, W.307, F.311, F.325, T.326 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: Q.136, F.137 Ligand excluded by PLIP EDO.9: 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.10: 4 residues within 4Å: Chain A: K.21, E.85, K.88, N.89 Ligand excluded by PLIP EDO.11: 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.12: 5 residues within 4Å: Chain A: R.57, V.103, E.110, L.423 Ligands: EDO.17 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: P.352, A.353, K.354, A.524, Q.525 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: N.185, H.192, G.256 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: K.131, T.172, L.173, K.174, I.396, N.397 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: I.345, V.501, L.533, A.534, I.536, A.537 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: P.52, T.106, A.107, G.108, V.109 Ligands: EDO.12 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: E.6, G.278, W.279, K.280, Y.281 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: Y.505, E.508, R.509 Ligands: EDO.21, EDO.39 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: R.538, Q.592 Ligands: EDO.39 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: R.509, D.511, K.591 Ligands: EDO.19 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain B: F.375, G.377, T.388, W.390, S.393, N.403, Y.404, Y.430 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: P.52, R.57, T.106, A.107, G.108, V.109, E.110 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: S.559, E.560, F.645, F.650 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: K.131, T.172, L.173, K.174, I.396, N.397 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain B: L.435, D.462, P.475, V.476, V.479, R.492, I.517, A.613, G.614 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: A.55, W.307, F.311, F.325, T.326 Ligands: EDO.37 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain B: A.135, D.399, A.401 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: Y.182, D.184, F.197, D.199, T.201 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain A: K.23 Chain B: E.468 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain B: K.21, K.88, Q.92 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: L.389, S.393, K.394, A.395, E.398, H.406 Ligand excluded by PLIP EDO.35: 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.36: 3 residues within 4Å: Chain B: R.358, P.384, Y.385 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: S.53, A.55, M.329, K.330 Ligands: EDO.27 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain B: K.254, D.259, A.263, P.264, L.265 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Ligands: EDO.19, EDO.20 Ligand excluded by PLIP EDO.40: 5 residues within 4Å: Chain B: I.246, F.249, G.250, A.255, Q.276 Ligand excluded by PLIP

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.7 CA.29: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: TPP.28 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.42

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, 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: CA.2 22 PLIP interactions: 16 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.116, A:I.189, B:L.382, B:V.409, B:F.437, B:Y.440 Hydrogen bonds: A:G.114, A:L.116, A:D.155, A:G.156, A:E.160, A:N.185 Water bridges: A:A.29, A:C.157, A:D.183, A:D.183, A:N.185, B:E.411 Salt bridges: A:H.66, A:H.66, A:H.261 pi-Stacking: B:F.437 TPP.28: 23 residues within 4Å: Chain A: D.381, L.382, V.409, E.411, F.434, F.437, Y.440, H.473 Chain B: A.29, H.66, 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: CA.29 22 PLIP interactions: 16 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.116, B:I.189, A:L.382, A:V.409, A:F.437, A:Y.440 Hydrogen bonds: B:G.114, B:L.116, B:D.155, B:G.156, B:E.160, B:N.185 Water bridges: B:A.29, B:N.64, B:C.157, B:D.183, B:D.183, A:E.411 Salt bridges: B:H.66, B:H.66, B:H.261 pi-Stacking: A:F.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Affaticati, P.E. et al., Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes. Sci Rep (2016)

Release Date

2016-11-02

Peptides

Transketolase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transketolase 1