SMTL ID : 3m34.1

Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Q.12, S.46, Y.47, R.292, F.293, S.295, A.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.12, A:S.46, A:S.295, A:A.296 GOL.2: 4 residues within 4Å: Chain A: R.344, S.371, H.444, R.502 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.344, A:R.344, A:H.444, A:R.502 GOL.6: 7 residues within 4Å: Chain B: Q.12, S.46, Y.47, R.292, F.293, S.295, A.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.12, B:S.46, B:S.295, B:A.296 GOL.7: 4 residues within 4Å: Chain B: R.344, S.371, H.444, R.502 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.344, B:R.344, B:H.444, B:R.502

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.1 CA.8: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: TPP.10 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.17

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

EDO.4: 5 residues within 4Å: Chain A: Y.596, K.597, F.598, C.599, H.600 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.596 Water bridges: A:L.580, A:H.600 EDO.9: 5 residues within 4Å: Chain B: Y.596, K.597, F.598, C.599, H.600 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.596 Water bridges: B:L.580, B:H.600

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.5: 21 residues within 4Å: Chain A: A.34, H.70, G.117, P.118, L.119, G.154, D.155, G.156, E.160, N.185, I.187, I.189, I.245, H.259 Chain B: D.367, I.392, E.394, F.420, Y.423, H.456 Ligands: CA.3 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:L.119, A:I.189, B:D.367, B:I.392, B:F.420, B:Y.423 Hydrogen bonds: A:G.117, A:L.119, A:D.155, A:D.155, A:G.156, A:E.160, A:N.185 Water bridges: A:A.34, A:G.154, B:E.394 Salt bridges: A:H.70, A:H.70, A:H.259 pi-Stacking: B:F.420 TPP.10: 21 residues within 4Å: Chain A: D.367, I.392, E.394, F.420, Y.423, H.456 Chain B: A.34, H.70, G.117, P.118, L.119, G.154, D.155, G.156, E.160, N.185, I.187, I.189, I.245, H.259 Ligands: CA.8 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.119, B:I.189, A:D.367, A:I.392, A:F.420, A:Y.423 Hydrogen bonds: B:G.117, B:L.119, B:D.155, B:G.156, B:N.185 Water bridges: B:A.34, B:G.154 Salt bridges: B:H.70, B:H.70, B:H.259 pi-Stacking: A:F.420

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal structure of transketolase in complex with thiamin diphosphate and calcium ion. To be Published

Release Date

2010-04-28

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

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