5INJ

Crystal Structure of Prenyltransferase PriB Ternary Complex with L-Tryptophan and Dimethylallyl thiolodiphosphate (DMSPP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Structure and specificity of a permissive bacterial C-prenyltransferase.

Elshahawi, S.I.Cao, H.Shaaban, K.A.Ponomareva, L.V.Subramanian, T.Farman, M.L.Spielmann, H.P.Phillips, G.N.Thorson, J.S.Singh, S.

(2017) Nat Chem Biol 13: 366-368

  • DOI: 10.1038/nchembio.2285
  • Primary Citation of Related Structures:  
    5INJ, 5JXM, 5K9M

  • PubMed Abstract: 
  • This study highlights the biochemical and structural characterization of the L-tryptophan C6 C-prenyltransferase (C-PT) PriB from Streptomyces sp. RM-5-8. PriB was found to be uniquely permissive to a diverse array of prenyl donors and acceptors including daptomycin ...

    This study highlights the biochemical and structural characterization of the L-tryptophan C6 C-prenyltransferase (C-PT) PriB from Streptomyces sp. RM-5-8. PriB was found to be uniquely permissive to a diverse array of prenyl donors and acceptors including daptomycin. Two additional PTs also produced novel prenylated daptomycins with improved antibacterial activities over the parent drug.


    Organizational Affiliation

    Center for Pharmaceutical Research and Innovation (CPRI), University of Kentucky, Lexington, Kentucky, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PrenyltransferaseA405Streptomyces sp. RM-5-8Mutation(s): 0 
UniProt
Find proteins for A0A182DWE5 (Streptomyces sp. RM-5-8)
Explore A0A182DWE5 
Go to UniProtKB:  A0A182DWE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A182DWE5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DST
Query on DST

Download Ideal Coordinates CCD File 
D [auth A]DIMETHYLALLYL S-THIOLODIPHOSPHATE
C5 H12 O6 P2 S
ZWFWSISPSBLNGO-UHFFFAOYSA-N
 Ligand Interaction
TRP
Query on TRP

Download Ideal Coordinates CCD File 
B [auth A]TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.163 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.396α = 90
b = 83.422β = 106.74
c = 41.618γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AutoSolphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM098248
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA84374
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)United StatesUL1TR000117

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 1.3: 2017-03-29
    Changes: Database references
  • Version 1.4: 2017-09-27
    Changes: Author supporting evidence
  • Version 2.0: 2019-10-02
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.2: 2020-09-23
    Changes: Structure summary