2P5S | pdb_00002p5s

RAB domain of human RASEF in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb2P5S/pdb

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


• Deposited: 2007-03-16 Released: 2007-03-27 
• Deposition Author(s): Zhu, H., Wang, J., Shen, Y., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.260 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.214 (DCC) 

Starting Model: experimental

Literature

RAB domain of human RASEF in complex with GDP

Zhu, H., Wang, J., Shen, Y., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 45.02 kDa 
• Atom Count: 2,527 
• Modeled Residue Count: 318 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAS and EF-hand domain containing	A, B	199	Homo sapiens	Mutation(s): 0  Gene Names: RASEF EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IZ41 (Homo sapiens) Explore Q8IZ41  Go to UniProtKB:  Q8IZ41
PHAROS:  Q8IZ41 GTEx:  ENSG00000165105

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], E [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
UNX	D [auth A], F [auth B], G [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.260 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.214 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.275	α = 90
b = 42.524	β = 98.91
c = 75.656	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Zhu, H., Wang, J., Shen, Y., Tempel, W., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description