› 2dcn

X-ray diffraction
2.25Å resolution

Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate (alpha-furanose form)

Released:
DOI: 10.2210/pdb2dcn/pdb
PDB entry 2dcn coloured by chain, front view.
PDB entry 2dcn coloured by chain, side view.
PDB entry 2dcn coloured by chain, top view.
Source organism: Sulfurisphaera tokodaii str. 7
Entry authors: Okazaki S, Onda H, Suzuki A, Kuramitsu S, Masui R, Yamane T

Function and Biology Details

Reaction catalysed: 
ATP + 2-dehydro-3-deoxy-D-gluconate = ADP + 2-dehydro-3-deoxy-6-phospho-D-gluconate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188783 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
2-dehydro-3-deoxygluconokinase Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 311 amino acids
Theoretical weight: 34.52 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96XN9 (Residues: 1-311; Coverage: 100%)
Gene names: ST2478, STK_24780, kdgK
Sequence domains: pfkB family carbohydrate kinase
Structure domains: UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase

Ligands and Environments

4 bound ligands:
Ligand MG 44 x MG
Ligand K 12 x K
Ligand CKP 12 x CKP
Ligand ADP 12 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 84.638Å b: 150.229Å c: 154.757Å
α: 90° β: 93.73° γ: 90°
R-values:
R R work R free
0.178 0.175 0.228
Expression system: Escherichia coli

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