4KLZ

Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis

• PDB DOI: https://doi.org/10.2210/pdb4KLZ/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-07 Released: 2014-09-17 
• Deposition Author(s): Shah, D.M., Kobayashi, M., Keizers, P.H., Tuin, A.W., Ab, E., Manning, L., Rzepiela, A.A., Andrews, M., Hoedemaeker, F.J., Siegal, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach applied to Rit1, a Target for Rheumatoid Arthritis

Shah, D.M., Kobayashi, M., Keizers, P.H., Tuin, A.W., Ab, E., Manning, L., Rzepiela, A.A., Andrews, M., Hoedemaeker, F.J., Siegal, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 20.55 kDa 
• Atom Count: 1,336 
• Modelled Residue Count: 156 
• Deposited Residue Count: 173 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Rit1	A	173	Homo sapiens	Mutation(s): 0  Gene Names: RIT1, RIBB, RIT, ROC1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92963 (Homo sapiens) Explore Q92963  Go to UniProtKB:  Q92963
PHAROS:  Q92963 GTEx:  ENSG00000143622

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.311 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.278	α = 90
b = 37.048	β = 95.9
c = 40.736	γ = 90

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
Coot	model building
REFMAC	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-17 
Deposition Author(s): Shah, D.M., Kobayashi, M., Keizers, P.H., Tuin, A.W., Ab, E., Manning, L., Rzepiela, A.A., Andrews, M., Hoedemaeker, F.J., Siegal, G.

Revision History  

• Version 1.0: 2014-09-17
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description