3MSX

Crystal structure of RhoA.GDP.MgF3 in complex with GAP domain of ArhGAP20

• PDB DOI: https://doi.org/10.2210/pdb3MSX/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-04-29 Released: 2011-03-16 
• Deposition Author(s): Utepbergenov, D., Cooper, D.R., Derewenda, U., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Literature

Mechanism of molecular specificity of RhoGAP domains towards small GTPases of RhoA family.

Utepbergenov, D., Cooper, D.R., Derewenda, U., Somlyo, A.V., Derewenda, Z.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.49 kDa 
• Atom Count: 3,193 
• Modelled Residue Count: 369 
• Deposited Residue Count: 381 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	A	180	Homo sapiens	Mutation(s): 1  Gene Names: ARH12, ARHA, RHO12, RHOA EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens) Explore P61586  Go to UniProtKB:  P61586
PHAROS:  P61586 GTEx:  ENSG00000067560

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho GTPase-activating protein 20	B	201	Homo sapiens	Mutation(s): 0  Gene Names: ARHGAP20, KIAA1391
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2F6 (Homo sapiens) Explore Q9P2F6  Go to UniProtKB:  Q9P2F6
PHAROS:  Q9P2F6 GTEx:  ENSG00000137727

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MGF	E [auth A]	TRIFLUOROMAGNESATE F3 Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.057	α = 90
b = 88.977	β = 90
c = 137.725	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Utepbergenov, D., Cooper, D.R., Derewenda, U., Derewenda, Z.S.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2021-10-06
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-21
  Changes: Data collection