2CLS

The crystal structure of the human RND1 GTPase in the active GTP bound state

• PDB DOI: https://doi.org/10.2210/pdb2CLS/pdb

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


• Deposited: 2006-04-28 Released: 2006-05-04 
• Deposition Author(s): Pike, A.C.W., Yang, X., Colebrook, S., Gileadi, O., Sobott, F., Bray, J., Wen Hwa, L., Marsden, B., Zhao, Y., Schoch, G., Elkins, J., Debreczeni, J.E., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

The Crystal Structure of the Human Rnd1 Gtpase in the Active GTP Bound State

Pike, A.C.W., Yang, X., Colebrook, S., Gileadi, O., Sobott, F., Bray, J., Wen Hwa, L., Marsden, B., Zhao, Y., Schoch, G., Elkins, J., Debreczeni, J.E., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 45.31 kDa 
• Atom Count: 2,918 
• Modelled Residue Count: 357 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RHO-RELATED GTP-BINDING PROTEIN RHO6	A, B	198	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92730 (Homo sapiens) Explore Q92730  Go to UniProtKB:  Q92730
PHAROS:  Q92730 GTEx:  ENSG00000172602

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	C [auth A], E [auth B]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.236 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.168	α = 90
b = 67.762	β = 90
c = 206.409	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-04 
Deposition Author(s): Pike, A.C.W., Yang, X., Colebrook, S., Gileadi, O., Sobott, F., Bray, J., Wen Hwa, L., Marsden, B., Zhao, Y., Schoch, G., Elkins, J., Debreczeni, J.E., Turnbull, A.P., von Delft, F., Arrowsmith, C., Edwards, A., Weigelt, J., Sundstrom, M., Doyle, D.

Revision History  

• Version 1.0: 2006-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description