4YP9

Crystal Structure of LuxP In Complex With a Formose Derived AI-2 Analogue


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report



Literature

Discovery of Glycomimetic Agonists from a Protocell Metabolism, Proto-natural Product Libraries

Sattin, S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Autoinducer 2-binding periplasmic protein LuxPAB345Vibrio harveyiMutation(s): 0 
Gene Names: luxP
Find proteins for P54300 (Vibrio harveyi)
Explore P54300 
Go to UniProtKB:  P54300
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A1B
Query on A1B

Download Ideal Coordinates CCD File 
A, B
1-deoxy-alpha-L-xylulofuranose-1,2-borate
C5 H10 B O6
GNABZUZRGYHKDZ-VPENINKCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.732α = 90
b = 104.732β = 90
c = 69.532γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/D023343/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/D023327/1
Engineering and Physical Sciences Research CouncilUnited KingdomEP/E000614/1
Royal SocietyUnited Kingdom--

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 2.0: 2017-09-13
    Changes: Atomic model, Author supporting evidence, Derived calculations, Non-polymer description, Structure summary