1OW3

Crystal Structure of RhoA.GDP.MgF3-in Complex with RhoGAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

MgF(3)(-) as a Transition State Analog of Phosphoryl Transfer

Graham, D.L.Lowe, P.N.Grime, G.W.Marsh, M.Rittinger, K.Smerdon, S.J.Gamblin, S.J.Eccleston, J.F.

(2002) Chem Biol 9: 375-381

  • DOI: https://doi.org/10.1016/s1074-5521(02)00112-6
  • Primary Citation of Related Structures:  
    1OW3

  • PubMed Abstract: 

    The formation of complexes between small G proteins and certain of their effectors can be facilitated by aluminum fluorides. Solution studies suggest that magnesium may be able to replace aluminum in such complexes. We have determined the crystal structure of RhoA.GDP bound to RhoGAP in the presence of Mg(2+) and F(-) but without Al(3+). The metallofluoride adopts a trigonal planar arrangement instead of the square planar structure of AlF(4)(-). We have confirmed that these crystals contain magnesium and not aluminum by proton-induced X-ray emission spectroscopy. The structure adopted by GDP.MgF(-) possesses the stereochemistry and approximate charge expected for the transition state. We suggest that MgF3(-) may be the reagent of choice for studying phosphoryl transfer reactions.


  • Organizational Affiliation

    Computational & Structural Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rho-GTPase-activating protein 1242Homo sapiensMutation(s): 0 
Gene Names: RHOGAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q07960 (Homo sapiens)
Go to UniProtKB:  Q07960
PHAROS:  Q07960
GTEx:  ENSG00000175220 
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming protein RhoA193Homo sapiensMutation(s): 1 
Gene Names: RHOA
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens)
Go to UniProtKB:  P61586
PHAROS:  P61586
GTEx:  ENSG00000067560 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MGF
Query on MGF

Download Ideal Coordinates CCD File 
E [auth B]TRIFLUOROMAGNESATE
F3 Mg
GJOMWUHGUQLOAC-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.49α = 90
b = 71.4β = 90
c = 91.15γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-06
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-04-16
    Changes: Data collection
  • Version 1.4: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description