6TKZ | pdb_00006tkz

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

• PDB DOI: https://doi.org/10.2210/pdb6TKZ/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.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom), Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content 

• Total Structure Weight: 149.06 kDa 
• Atom Count: 9,582 
• Modeled Residue Count: 1,188 
• Deposited Residue Count: 1,292 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dedicator of cytokinesis protein 10	A [auth B], 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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	E [auth C], F [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
GOL (Subject of Investigation/LOI)	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.17	α = 90
b = 97.17	β = 90
c = 312	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.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	MC_UP_1201/6
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 2.0: 2022-09-07
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
• Version 2.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description