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 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hypothetical fructokinase
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
311Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Gene Names: kdgKST2478STK_24780
EC: 2.7.1.45
UniProt
Find proteins for Q96XN9 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q96XN9 
Go to UniProtKB:  Q96XN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96XN9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth B],
AC [auth J],
GA [auth C],
GC [auth K],
HB [auth G],
AA [auth B],
AC [auth J],
GA [auth C],
GC [auth K],
HB [auth G],
NA [auth D],
NB [auth H],
NC [auth L],
T [auth A],
TA [auth E],
TB [auth I],
YA [auth F]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CKP
Query on CKP

Download Ideal Coordinates CCD File 
FA [auth C],
FC [auth K],
GB [auth G],
MA [auth D],
MB [auth H],
FA [auth C],
FC [auth K],
GB [auth G],
MA [auth D],
MB [auth H],
MC [auth L],
S [auth A],
SA [auth E],
SB [auth I],
XA [auth F],
Z [auth B],
ZB [auth J]
6-O-phosphono-beta-D-psicofuranosonic acid
C6 H11 O10 P
LXQWHMQOSMCJIZ-ZGEUXELVSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
EA [auth C],
EC [auth K],
FB [auth G],
LA [auth D],
LB [auth H],
EA [auth C],
EC [auth K],
FB [auth G],
LA [auth D],
LB [auth H],
LC [auth L],
R [auth A],
RA [auth E],
RB [auth I],
WA [auth F],
Y [auth B],
YB [auth J]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth G],
BA [auth C],
BB [auth G],
BC [auth K],
CA [auth C],
AB [auth G],
BA [auth C],
BB [auth G],
BC [auth K],
CA [auth C],
CB [auth G],
CC [auth K],
DA [auth C],
DB [auth G],
DC [auth K],
EB [auth G],
HA [auth D],
HC [auth L],
IA [auth D],
IB [auth H],
IC [auth L],
JA [auth D],
JB [auth H],
JC [auth L],
KA [auth D],
KB [auth H],
KC [auth L],
M [auth A],
N [auth A],
O [auth A],
OA [auth E],
OB [auth I],
P [auth A],
PA [auth E],
PB [auth I],
Q [auth A],
QA [auth E],
QB [auth I],
U [auth B],
UA [auth F],
UB [auth J],
V [auth B],
VA [auth F],
VB [auth J],
W [auth B],
WB [auth J],
X [auth B],
XB [auth J],
ZA [auth G]
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 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.638α = 90
b = 150.229β = 93.73
c = 154.757γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-31
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-05-24
    Changes: Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Derived calculations, Structure summary