5QQI | pdb_00005qqi

PanDDA analysis group deposition -- Crystal Structure of Kalirin/Rac1 in complex with MolPort-009-178-994

• PDB DOI: https://doi.org/10.2210/pdb5QQI/pdb
• Deposition Group: G_1002072 (changed state) | Explore  G_1002072  

• Classification: Hydrolase/Transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-05-03 Released: 2019-12-18 
• Deposition Author(s): Gray, J.L., Krojer, T., Talon, R., Douangamath, A., Jimenez Antunez, C., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P.E., von Delft, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.277 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

PanDDA analysis group deposition

Gray, J.L., Krojer, T., Talon, R., Douangamath, A., Jimenez Antunez, C., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P.E., 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)

Macromolecule Content 

• Total Structure Weight: 41.4 kDa 
• Atom Count: 3,135 
• Modeled Residue Count: 356 
• Deposited Residue Count: 360 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	A	178	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	182	Homo sapiens	Mutation(s): 0  Gene Names: KALRN, DUET, DUO, HAPIP, TRAD EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for O60229 (Homo sapiens) Explore O60229  Go to UniProtKB:  O60229
PHAROS:  O60229 GTEx:  ENSG00000160145

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N6D	D [auth A]	N-[3-(methoxymethyl)phenyl]-N'-(5-methyl-1,2-oxazol-3-yl)urea C13 H15 N3 O3 YVOJGWYXMJROLU-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.277 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.505	α = 90
b = 62.505	β = 90
c = 341.296	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-18 
Deposition Author(s): Gray, J.L., Krojer, T., Talon, R., Douangamath, A., Jimenez Antunez, C., Bountra, C., Arrowsmith, C.H., Edwards, A., Brennan, P.E., von Delft, F.

Revision History  

• Version 1.0: 2019-12-18
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references
• Version 1.2: 2026-02-18
  Changes: Refinement description, Structure summary