SMTL ID : 4zu7.2 (3 other biounits)

X-ray structure if the QdtA 3,4-ketoisomerase from Thermoanaerobacterium thermosaccharolyticum, double mutant Y17R/R97H, in complex with TDP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 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, Y.116, Y.121, R.123 Chain B: I.13, R.17, P.22 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.37 Hydrogen bonds: A:R.35, A:G.49, A:Y.121 Salt bridges: A:R.48, A:H.51, A:R.123, B:R.17, B:R.17 pi-Stacking: A:Y.116 Water bridges: B:R.17, B:R.17 TYD.2: 13 residues within 4Å: Chain A: I.13, R.17, L.20, P.22 Chain B: R.35, Y.37, I.39, R.48, G.49, H.51, Y.116, Y.121, R.123 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Y.37, B:Y.116, A:L.20 Hydrogen bonds: B:R.35, B:G.49, B:H.51, B:Y.121 Salt bridges: B:R.48, B:H.51, B:R.123, A:R.17, A:R.17 pi-Stacking: B:Y.116

1 x PXN: (2S)-1-[3-{[(2R)-2-hydroxypropyl]oxy}-2,2-bis({[(2R)-2-hydroxypropyl]oxy}methyl)propoxy]propan-2-ol(Non-covalent)

PXN.3: 4 residues within 4Å: Chain B: Y.50, K.72, E.98, Y.125 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.125, B:Y.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Bacterial Sugar 3,4-Ketoisomerases: Structural Insight into Product Stereochemistry. Biochemistry (2015)

Release Date

2015-07-15

Peptides

QdtA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

QdtA

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