2ERX | pdb_00002erx

Crystal Structure of DiRas2 in Complex With GDP and Inorganic Phosphate

• PDB DOI: https://doi.org/10.2210/pdb2ERX/pdb

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


• Deposited: 2005-10-25 Released: 2005-11-01 
• Deposition Author(s): Papagrigoriou, E., Yang, X., Elkins, J., Niesen, F.E., Burgess, N., Salah, E., Fedorov, O., Ball, L.J., von Delft, F., Sundstrom, M., Edwards, A., Arrowsmith, C., Weigelt, J., Doyle, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.188 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of DiRas2

Papagrigoriou, E., Yang, X., Elkins, J., Niesen, F.E., Burgess, N., Salah, E., Fedorov, O., Ball, L.J., von Delft, F., Sundstrom, M., Edwards, A., Arrowsmith, C., Weigelt, J., Doyle, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 39.8 kDa 
• Atom Count: 2,816 
• Modelled Residue Count: 334 
• Deposited Residue Count: 344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Di-Ras2	A, B	172	Homo sapiens	Mutation(s): 0  Gene Names: DIRAS2 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HU8 (Homo sapiens) Explore Q96HU8  Go to UniProtKB:  Q96HU8
PHAROS:  Q96HU8 GTEx:  ENSG00000165023

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	E [auth A], H [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4	C [auth A], F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.188 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.041	α = 90
b = 74.931	β = 90
c = 85.691	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-01 
Deposition Author(s): Papagrigoriou, E., Yang, X., Elkins, J., Niesen, F.E., Burgess, N., Salah, E., Fedorov, O., Ball, L.J., von Delft, F., Sundstrom, M., Edwards, A., Arrowsmith, C., Weigelt, J., Doyle, D.

Revision History  

• Version 1.0: 2005-11-01
  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: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary