SMTL ID : 3m6l.1

Crystal structure of transketolase in complex with thiamine diphosphate, ribose-5-phosphate and calcium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

homo-dimer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: Q.12, S.46, Y.47, R.292, F.293, S.295, A.296, L.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.12, A:S.46, A:A.296 Water bridges: A:F.293 GOL.7: 8 residues within 4Å: Chain B: Q.12, S.46, Y.47, R.292, F.293, S.295, A.296, L.299 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.12, B:S.46, B:A.296 Water bridges: B:F.293

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 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: CA.3, R5P.5 18 PLIP interactions: 5 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:D.367, B:I.392, B:F.420, B:Y.423, A:L.119, A:I.189 pi-Stacking: B:F.420 Hydrogen bonds: A:G.117, A:L.119, A:D.155, A:G.156, A:N.185 Water bridges: A:A.34, A:H.70, A:G.154 Salt bridges: A:H.70, A:H.70, A:H.259 TPP.8: 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: CA.9, R5P.11 21 PLIP interactions: 6 interactions with chain A, 15 interactions with chain B Hydrophobic interactions: A:D.367, A:I.392, A:F.420, A:Y.423, B:L.119, B:I.189 Water bridges: A:E.394, B:A.34, B:H.70, B:G.154 pi-Stacking: A:F.420 Hydrogen bonds: B:G.117, B:L.119, B:D.155, B:D.155, B:G.156, B:E.160, B:N.185 Salt bridges: B:H.70, B:H.70, B:H.259

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 4 residues within 4Å: Chain A: D.155, N.185, I.187 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.155, A:I.187, H2O.7 CA.9: 4 residues within 4Å: Chain B: D.155, N.185, I.187 Ligands: TPP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.155, B:I.187, H2O.28

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

EDO.4: 5 residues within 4Å: Chain A: L.580, Y.596, K.597, F.598, H.600 No protein-ligand interaction detected (PLIP) EDO.10: 5 residues within 4Å: Chain B: L.580, Y.596, K.597, F.598, H.600 No protein-ligand interaction detected (PLIP)

2 x R5P: RIBOSE-5-PHOSPHATE(Non-covalent)

R5P.5: 12 residues within 4Å: Chain A: H.31, H.104, I.189, H.259 Chain B: R.344, S.371, F.417, H.444, D.452, H.456, R.502 Ligands: TPP.2 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.371, B:D.452, A:H.259 Water bridges: B:S.371, B:R.502, B:R.502, A:R.95 Salt bridges: B:R.344, B:H.444, B:R.502 R5P.11: 12 residues within 4Å: Chain A: R.344, S.371, F.417, H.444, D.452, H.456, R.502 Chain B: H.31, H.104, I.189, H.259 Ligands: TPP.8 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.371, A:D.452, B:H.259 Water bridges: A:S.371, A:R.502, A:R.502, B:R.95 Salt bridges: A:R.344, A:H.444, A:R.502

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 3 residues within 4Å: Chain A: H.284, P.286, Q.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.287 Water bridges: A:I.285 Salt bridges: A:H.284 PO4.12: 3 residues within 4Å: Chain B: H.284, P.286, Q.287 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.287 Water bridges: B:I.285 Salt bridges: B:H.284

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 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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