5O33 | pdb_00005o33

A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1

• PDB DOI: https://doi.org/10.2210/pdb5O33/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-23 Released: 2017-05-31 
• Deposition Author(s): Gray, J., Krojer, T., Talon, R., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

A structure of the GEF Kalirin DH1 domain in complex with the small GTPase Rac1

Gray, J., Krojer, T., Talon, R., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P., von Delft, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 41.58 kDa 
• Atom Count: 3,144 
• Modeled Residue Count: 356 
• Deposited Residue Count: 357 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	A	177	Homo sapiens	Mutation(s): 0  Gene Names: RAC1, TC25, MIG5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
PHAROS:  P63000 GTEx:  ENSG00000136238

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kalirin	B	180	Rattus norvegicus	Mutation(s): 0  Gene Names: Kalrn, Duo, Hapip EC: 2.7.11.1
UniProt
Find proteins for P97924 (Rattus norvegicus) Explore P97924  Go to UniProtKB:  P97924

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.255	α = 90
b = 63.255	β = 90
c = 346.704	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Gray, J., Krojer, T., Talon, R., Fairhead, M., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P., von Delft, F.

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description