6TKY

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

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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

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

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

(2022) Biorxiv 


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dedicator of cytokinesis protein 10A [auth B]457Homo sapiensMutation(s): 0 
Gene Names: DOCK10, KIAA0694, ZIZ3
UniProt & NIH Common Fund Data Resources
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Go to UniProtKB:  Q96BY6
PHAROS:  Q96BY6
Entity Groups  
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UniProt GroupQ96BY6
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 42 homologB [auth C],
C [auth D]		188Homo sapiensMutation(s): 0 
Gene Names: CDC42
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60953 (Homo sapiens)
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PHAROS:  P60953
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UniProt GroupP60953
Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Dedicator of cytokinesis protein 10D [auth A]458Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96BY6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL (Subject of Investigation/LOI)
Query on GOL
Download Ideal Coordinates CCD File 
E [auth D],
F [auth A],
G [auth A]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
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 = 96.898α = 90
b = 96.898β = 90
c = 310.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC576/A14109

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2022-06-29
    Changes: Database references