1U5D

Crystal Structure of the PH domain of SKAP55

• PDB DOI: https://doi.org/10.2210/pdb1U5D/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2004-07-27 Released: 2005-07-26 
• Deposition Author(s): Tang, Y., Swanson, K.D., Neel, B.G., Eck, M.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.185 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Structural Basis for the Dimerization and Phosphoinositide Specificity of the Src Kinase-associated Phosphoproteins SKAP55 and SKAP-Hom

Tang, Y., Swanson, K.D., Neel, B.G., Eck, M.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 5 generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 6 generated by PISA (software)

Biological Assembly 7  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 7 generated by PISA (software)

Biological Assembly 8  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 8 generated by PISA (software)

Biological Assembly 9  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 9 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.57 kDa 
• Atom Count: 4,040 
• Modelled Residue Count: 430 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Src Kinase-associated Phosphoprotein of 55 kDa	A, B, C, D	108	Homo sapiens	Mutation(s): 2  Gene Names: HSSKAP55 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q86WV1 (Homo sapiens) Explore Q86WV1  Go to UniProtKB:  Q86WV1
PHAROS:  Q86WV1 GTEx:  ENSG00000141293

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], J [auth D], K [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.185 
• R-Value Work: 0.168 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.068	α = 90
b = 33.352	β = 110.31
c = 105.382	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Tang, Y., Swanson, K.D., Neel, B.G., Eck, M.J.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description