2Q3F | pdb_00002q3f

X-ray crystal structure of putative human Ras-related GTP binding D in complex with GMPPNP

• PDB DOI: https://doi.org/10.2210/pdb2Q3F/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-05-30 Released: 2007-06-12 
• Deposition Author(s): Mulichak, A.M., Rabeh, W.M., Tempel, W., Nedyalkova, L., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Keefe, L.J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.268 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Literature

Crystal structure of human Ras-related GTP-binding D.

Mulichak, A.M., Rabeh, W.M., Tempel, W., Nedyalkova, L., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Keefe, L.J., Bochkarev, A., Park, H.

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: 43.35 kDa 
• Atom Count: 3,032 
• Modeled Residue Count: 357 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related GTP-binding protein D	A, B	181	Homo sapiens	Mutation(s): 4  Gene Names: RRAGD EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQL2 (Homo sapiens) Explore Q9NQL2  Go to UniProtKB:  Q9NQL2
PHAROS:  Q9NQL2 GTEx:  ENSG00000025039

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	D [auth A], F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.268 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.73	α = 90
b = 67.13	β = 110.92
c = 66.36	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Mulichak, A.M., Rabeh, W.M., Tempel, W., Nedyalkova, L., Landry, R., Arrowsmith, C.H., Edwards, A.M., Sundstrom, M., Weigelt, J., Keefe, L.J., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-06-12
  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: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary