SMTL ID : 3m7i.1

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate(pyranose form) and magnesium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 23 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, S.188, I.189, I.245, H.259 Chain B: D.367, I.392, E.394, F.420, Y.423, H.456 Ligands: MG.3, RP5.4 20 PLIP interactions: 14 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: 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, A:N.185, B:E.394 Salt bridges: A:H.70, A:H.70, A:H.259 pi-Stacking: B:F.420 TPP.5: 23 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, S.188, I.189, I.245, H.259 Ligands: MG.7, RP5.8 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: 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, B:N.185 Salt bridges: B:H.70, B:H.70, B:H.259 pi-Stacking: A:F.420

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

EDO.2: 5 residues within 4Å: Chain A: Y.596, K.597, F.598, C.599, H.600 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.597, A:H.600 EDO.6: 5 residues within 4Å: Chain B: Y.596, K.597, F.598, C.599, H.600 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.597, B:H.600

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.6 MG.7: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.19

2 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)

RP5.4: 11 residues within 4Å: Chain A: H.31, I.189, H.259, G.260 Chain B: R.344, S.371, F.417, H.444, D.452, R.502 Ligands: TPP.1 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.371, B:S.371, B:D.452, A:H.259 Salt bridges: B:R.344, B:H.444, B:H.456, B:R.502, A:H.31 RP5.8: 11 residues within 4Å: Chain A: R.344, S.371, F.417, H.444, D.452, R.502 Chain B: H.31, I.189, H.259, G.260 Ligands: TPP.5 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.371, A:S.371, A:D.452, B:H.259 Salt bridges: A:R.344, A:H.444, A:H.456, A:R.502, B:H.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate(pyranose form) and magnesium ion. TO BE PUBLISHED

Release Date

2010-04-07

Peptides

Transketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Transketolase

Related Entries With Identical Sequence