SMTL ID : 3mos.1

The structure of human Transketolase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 25 residues within 4Å: Chain A: S.38, K.73, H.75, G.121, S.122, L.123, G.152, D.153, G.154, E.155, E.158, N.183, L.185, G.186, Q.187, K.242, H.256 Chain B: D.339, T.340, I.362, E.364, F.390, R.393, Q.426 Ligands: CA.2 19 PLIP interactions: 4 interactions with chain B, 15 interactions with chain A Hydrophobic interactions: B:F.390 Hydrogen bonds: B:Q.426, A:G.121, A:L.123, A:D.153, A:D.153, A:G.154, A:E.155, A:N.183 Water bridges: B:T.386, A:N.183, A:N.183 pi-Stacking: B:F.390 Salt bridges: A:K.73, A:H.75, A:H.75, A:K.242, A:K.242, A:H.256 TPP.14: 25 residues within 4Å: Chain A: D.339, T.340, I.362, E.364, F.390, R.393, Q.426 Chain B: S.38, K.73, H.75, G.121, S.122, L.123, G.152, D.153, G.154, E.155, E.158, N.183, L.185, G.186, Q.187, K.242, H.256 Ligands: CA.15 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:G.121, B:L.123, B:D.153, B:G.154, B:E.155, A:Q.426 Water bridges: B:N.183, B:N.183 Salt bridges: B:K.73, B:H.75, B:H.75, B:K.242, B:K.242, B:H.256 Hydrophobic interactions: A:F.390 pi-Stacking: A:F.390

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: D.153, N.183, L.185 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.153, A:L.185, H2O.1 CA.15: 4 residues within 4Å: Chain B: D.153, N.183, L.185 Ligands: TPP.14 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.153, B:L.185, H2O.19

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

EDO.3: 7 residues within 4Å: Chain A: Q.125, S.369, V.372, Q.397, M.400, A.401, S.404 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Y.561, Y.562, E.563, V.587, N.588 Chain B: P.439, K.536 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: L.156, S.157, W.162 Chain B: W.162, E.163, A.166, F.207 Ligands: EDO.9 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: Q.187, S.254, W.255, H.256 Chain B: N.342 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: Y.562, L.585, A.586, N.588 Ligand excluded by PLIP EDO.8: 8 residues within 4Å: Chain A: R.19, S.23, A.82, A.85, E.86, E.92, L.95, K.281 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: L.156, S.157, W.162, L.193, Y.200, R.203 Chain B: F.207 Ligands: EDO.5 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: P.61, N.66, D.67, R.68, F.69, W.84, R.377 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: Q.8, K.9, A.12 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: F.69, V.70, L.71, L.80, F.115, T.116 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain B: Q.125, S.369, V.372, Q.397, M.400, A.401, S.404 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: P.439, K.536 Chain B: Y.561, Y.562, E.563, V.587, N.588 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain A: W.162, E.163, A.166, F.207 Chain B: L.156, S.157, W.162 Ligands: EDO.22 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: N.342 Chain B: Q.187, S.254, W.255, H.256 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: Y.562, L.585, A.586, N.588 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: R.19, S.23, A.82, A.85, E.86, E.92, L.95, K.281 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain A: F.207 Chain B: L.156, S.157, W.162, L.193, Y.200, R.203 Ligands: EDO.18 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: P.61, N.66, D.67, R.68, F.69, W.84, R.377 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain B: Q.8, K.9, A.12 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: F.69, V.70, L.71, L.80, F.115, T.116 Ligand excluded by PLIP

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

NA.13: 4 residues within 4Å: Chain A: N.409, A.459, T.462, C.466 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.409, A:A.459, A:T.462 NA.26: 4 residues within 4Å: Chain B: N.409, A.459, T.462, C.466 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.409, B:T.462, B:T.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitschke, L. et al., The crystal structure of human transketolase and new insights into its mode of action. J.Biol.Chem. (2010)

Release Date

2010-07-28

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase