2DCN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of 2-keto-3-deoxygluconate kinase from Sulfolobus tokodaii complexed with 2-keto-6-phosphogluconate

Okazaki, S.Onda, H.Suzuki, A.Kuramitsu, S.Masui, R.Yamane, T.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
hypothetical fructokinase
A, B, C, D, E, F, G, H, I, J, K, L
311Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)Mutation(s): 0 
Gene Names: kdgK (ST2478)
EC: 2.7.1.45
Find proteins for Q96XN9 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q96XN9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CKP
Query on CKP

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Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
(2R,3R,4S,5R)-2,3,4-TRIHYDROXY-5-[(PHOSPHONATOOXY)METHYL]TETRAHYDROFURAN-2-CARBOXYLIC ACID
2-KETO-6-PHOSPHATE-D-GLUCONIC ACID, ALPHA-FURANOSE FORM
C6 H11 O10 P
LXQWHMQOSMCJIZ-ZGEUXELVSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 84.638α = 90.00
b = 150.229β = 93.73
c = 154.757γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MLPHAREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-05-24
    Type: Structure summary