6NAZ

Crystal structure of DIRAS 2/3 chimera in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb6NAZ/pdb

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


• Deposited: 2018-12-06 Released: 2019-12-18 
• Deposition Author(s): Gilbert, Y.H., Reger, A., Sharma, R., Bast, J., Kim, C.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free: 
  0.332 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.270 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DIRAS 2/3 chimera in complex with GDP

Gilbert, Y.H., Reger, A., Sharma, R., Bast, C.R., Kim, C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.4 kDa 
• Atom Count: 1,212 
• Modelled Residue Count: 157 
• Deposited Residue Count: 199 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein Di-Ras2,GTP-binding protein Di-Ras3,GTP-binding protein Di-Ras2	A	199	Homo sapiens	Mutation(s): 0  Gene Names: DIRAS2, DIRAS3, ARHI, NOEY2, RHOI 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
Find proteins for O95661 (Homo sapiens) Explore O95661  Go to UniProtKB:  O95661
PHAROS:  O95661 GTEx:  ENSG00000162595
UniProt Groups	O95661Q96HU8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL	C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.08 Å
• R-Value Free:  0.332 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.270 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.03	α = 90
b = 92.03	β = 90
c = 86.52	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
pointless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Gilbert, Y.H., Reger, A., Sharma, R., Bast, J., Kim, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	RO1 CA135354
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	NCI P50 CA 83639

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description