3LL3

The crystal structure of ligand bound xylulose kinase from Lactobacillus acidophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of xylulose kinase from Lactobacillus acidophilus

Zhang, Z.Burley, S.K.Swaminathan, S.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gluconate kinase
A, B
504Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM)Mutation(s): 0 
Find proteins for Q5FM28 (Lactobacillus acidophilus (strain ATCC 700396 / NCK56 / N2 / NCFM))
Go to UniProtKB:  Q5FM28
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
XUL
Query on XUL

Download SDF File 
Download CCD File 
A
D-XYLULOSE
C5 H10 O5
ZAQJHHRNXZUBTE-WUJLRWPWSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
DXP
Query on DXP

Download SDF File 
Download CCD File 
A, B
1-DEOXY-D-XYLULOSE-5-PHOSPHATE
C5 H11 O7 P
AJPADPZSRRUGHI-RFZPGFLSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 57.889α = 84.75
b = 73.056β = 86.32
c = 82.872γ = 77.95
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
CBASSdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance