SMTL ID : 4kxw.1

Human transketolase in covalent complex with donor ketose D-xylulose-5-phosphate, crystal 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.97 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.155, N.185, L.187 Ligands: TPP.15 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:L.187, H2O.1 MG.18: 4 residues within 4Å: Chain B: D.155, N.185, L.187 Ligands: TPP.32 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:L.187, H2O.38

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

EDO.2: 8 residues within 4Å: Chain A: P.63, N.68, D.69, R.70, F.71, W.86, D.119, R.379 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: Y.564, L.587, A.588, N.590 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: L.158, W.164, L.195, Y.202, R.205 Chain B: F.209 Ligands: EDO.12 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: L.92, D.106, L.107, Q.115 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: N.590, R.591 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: Y.137, Y.141, Y.173 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: E.423, G.596, K.597 Chain B: A.33, R.101, K.102 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: R.21, A.84, A.87, E.88, E.94, L.97, K.283 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: F.142, D.333, R.334, R.358, T.382 Ligand excluded by PLIP EDO.12: 10 residues within 4Å: Chain A: L.158, S.159, W.164, R.205 Chain B: W.164, E.165, A.168, F.209 Ligands: EDO.5, EDO.14 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain A: S.159 Chain B: E.165, A.168, F.169, I.172, A.365 Ligands: EDO.12 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain B: P.63, N.68, D.69, R.70, F.71, W.86, D.119, R.379 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: Y.564, L.587, A.588, N.590 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain B: F.71, V.72, L.73, L.82, F.117, T.118 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: F.209 Chain B: L.158, W.164, L.195, Y.202, R.205 Ligands: EDO.29 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: L.92, D.106, L.107, Q.115 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: N.590, R.591 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: Y.137, Y.141, Y.173 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: A.33, R.101, K.102 Chain B: E.423, G.596, K.597 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain B: R.21, A.84, A.87, E.88, E.94, L.97, K.283 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: F.142, D.333, R.334, R.358, T.382 Ligand excluded by PLIP EDO.29: 10 residues within 4Å: Chain A: W.164, E.165, A.168, F.209 Chain B: L.158, S.159, W.164, R.205 Ligands: EDO.22, EDO.31 Ligand excluded by PLIP EDO.31: 7 residues within 4Å: Chain A: E.165, A.168, F.169, I.172, A.365 Chain B: S.159 Ligands: EDO.29 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.13: 4 residues within 4Å: Chain A: N.411, A.461, T.464, C.468 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.411, A:T.464, A:T.464 NA.30: 4 residues within 4Å: Chain B: N.411, A.461, T.464, C.468 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.411, B:N.411, B:T.464

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.15: 26 residues within 4Å: Chain A: S.40, K.75, H.77, G.123, S.124, L.125, G.154, D.155, G.156, E.157, E.160, N.185, L.187, G.188, Q.189, K.244, H.258 Chain B: D.341, T.342, I.364, E.366, F.392, R.395, Q.428 Ligands: MG.1, DX5.16 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.123, A:L.125, A:D.155, A:G.156, A:E.157, A:N.185, B:Q.428 Water bridges: A:N.185, B:T.388 Salt bridges: A:K.75, A:H.77, A:H.77, A:K.244, A:K.244, A:H.258 Hydrophobic interactions: B:F.392 pi-Stacking: B:F.392 TPP.32: 26 residues within 4Å: Chain A: D.341, T.342, I.364, E.366, F.392, R.395, Q.428 Chain B: S.40, K.75, H.77, G.123, S.124, L.125, G.154, D.155, G.156, E.157, E.160, N.185, L.187, G.188, Q.189, K.244, H.258 Ligands: MG.18, DX5.33 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.123, B:L.125, B:D.155, B:G.156, B:E.157, B:N.185, A:Q.428 Water bridges: B:N.185 Salt bridges: B:K.75, B:H.77, B:H.77, B:K.244, B:K.244, B:H.258 Hydrophobic interactions: A:F.392 pi-Stacking: A:F.392

4 x DX5: D-XYLITOL-5-PHOSPHATE(Non-covalent)

DX5.16: 14 residues within 4Å: Chain A: H.37, H.77, H.110, G.123, Q.189, H.258 Chain B: S.345, F.389, H.416, D.424, Q.428, R.474 Ligands: TPP.15, DX5.17 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:H.110, A:H.258, B:S.345, B:Q.428 Water bridges: A:H.77, A:K.260, A:K.260, B:R.318, B:R.318, B:R.474 Salt bridges: B:H.416, B:R.474 DX5.17: 10 residues within 4Å: Chain A: H.37, Q.189, H.258, G.259 Chain B: R.318, S.345, H.416, D.424, R.474 Ligands: DX5.16 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:H.258 Water bridges: A:K.260, A:K.260, B:R.318, B:R.318, B:R.318, B:R.318, B:N.344, B:R.474, B:R.474 Salt bridges: A:K.260, B:R.318, B:H.416, B:R.474 DX5.33: 14 residues within 4Å: Chain A: S.345, F.389, H.416, D.424, Q.428, R.474 Chain B: H.37, H.77, H.110, G.123, Q.189, H.258 Ligands: TPP.32, DX5.34 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:S.345, A:Q.428, B:H.77, B:H.110, B:H.258 Water bridges: A:R.318, A:R.318, A:D.424, A:R.474, B:H.77, B:K.260, B:K.260 Salt bridges: A:H.416, A:R.474 DX5.34: 10 residues within 4Å: Chain A: R.318, S.345, H.416, D.424, R.474 Chain B: H.37, Q.189, H.258, G.259 Ligands: DX5.33 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Water bridges: A:R.318, A:R.318, A:R.318, A:R.318, A:N.344, A:R.474, A:R.474, B:K.260, B:K.260 Salt bridges: A:R.318, A:H.416, A:R.474, B:K.260 Hydrogen bonds: B:H.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ludtke, S. et al., Sub-angstrom-resolution crystallography reveals physical distortions that enhance reactivity of a covalent enzymatic intermediate. Nat Chem (2013)

Release Date

2013-08-21

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

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