6TKY

Crystal structure of the DHR2 domain of DOCK10 in complex with CDC42

• PDB DOI: https://doi.org/10.2210/pdb6TKY/pdb

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


• Deposited: 2019-11-29 Released: 2020-01-22 
• Deposition Author(s): Barford, D., Fan, D., Cronin, N., Yang, J.
• Funding Organization(s): Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.246 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Structural basis for CDC42 and RAC activation by the dual specificity GEF DOCK10

Fan, D., Yang, J., Cronin, N., Barford, D.

(2022) bioRxiv 

• DOI: https://doi.org/10.1101/2022.06.15.496229

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: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.3 kDa 
• Atom Count: 9,543 
• Modelled Residue Count: 1,188 
• Deposited Residue Count: 1,291 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dedicator of cytokinesis protein 10	A [auth B]	457	Homo sapiens	Mutation(s): 0  Gene Names: DOCK10, KIAA0694, ZIZ3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BY6 (Homo sapiens) Explore Q96BY6  Go to UniProtKB:  Q96BY6
PHAROS:  Q96BY6 GTEx:  ENSG00000135905

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 42 homolog	B [auth C], C [auth D]	188	Homo sapiens	Mutation(s): 0  Gene Names: CDC42 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60953 (Homo sapiens) Explore P60953  Go to UniProtKB:  P60953
PHAROS:  P60953 GTEx:  ENSG00000070831

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Dedicator of cytokinesis protein 10	D [auth A]	458	Homo sapiens	Mutation(s): 0  Gene Names: DOCK10, KIAA0694, ZIZ3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96BY6 (Homo sapiens) Explore Q96BY6  Go to UniProtKB:  Q96BY6
PHAROS:  Q96BY6 GTEx:  ENSG00000135905

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	E [auth D], F [auth A], G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.246 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.898	α = 90
b = 96.898	β = 90
c = 310.91	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Barford, D., Fan, D., Cronin, N., Yang, J.

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Funding Organization	Location	Grant Number
Cancer Research UK	United Kingdom	C576/A14109

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2022-06-29
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description