SMTL ID : 4o9e.1

Crystal structure of QdtA, a sugar 3,4-ketoisemerase from Thermoanaerobacterium thermosaccharolyticum in complex with TDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x TYD: THYMIDINE-5'-DIPHOSPHATE(Non-covalent)

TYD.1: 12 residues within 4Å: Chain A: R.35, Y.37, I.39, R.48, G.49, H.51, M.99, Y.116, Y.121, R.123 Chain B: I.13, P.22 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.37, A:Y.116 Hydrogen bonds: A:R.35, A:G.49, A:Y.121 Water bridges: A:R.97, A:R.123, A:R.123, B:K.11 Salt bridges: A:R.48, A:H.51, A:H.51, A:R.123 pi-Stacking: A:Y.116 TYD.3: 12 residues within 4Å: Chain A: I.13, L.20, P.22 Chain B: R.35, Y.37, I.39, R.48, G.49, H.51, Y.116, Y.121, R.123 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.37, B:Y.116, A:L.20 Hydrogen bonds: B:R.35, B:G.49 Salt bridges: B:R.48, B:H.51, B:H.51, B:R.123 pi-Stacking: B:Y.116

1 x TDR: THYMINE(Non-covalent)

TDR.2: 2 residues within 4Å: Chain A: K.72, E.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.72, A:E.98 pi-Stacking: A:Y.125

1 x 4TD: (2S)-1-[3-[(2S)-2-oxidanylpropoxy]-2-[[(2S)-2-oxidanylpropoxy]methyl]-2-[[(2R)-2-oxidanylpropoxy]methyl]propoxy]propan-2-ol(Non-covalent)

4TD.4: 4 residues within 4Å: Chain B: Y.50, K.72, E.98, Y.125 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.50, B:Y.125, B:Y.125 Hydrogen bonds: B:E.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., The molecular architecture of QdtA, a sugar 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum. Protein Sci. (2014)

Release Date

2014-04-09

Peptides

QdtA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

QdtA

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