4AZ9 | pdb_00004az9

Crystal structure of phox homology domain of human sorting nexin 24

• PDB DOI: https://doi.org/10.2210/pdb4AZ9/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-06-24 Released: 2012-10-10 
• Deposition Author(s): Oberholzer, A.E., Kiyani, W., Krojer, T., Shrestha, L., von Delft, F., Froese, D.S., Chaikuad, A., Raynor, J., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Crystal Structure of Phox Homology Domain of Human Sorting Nexin 24

Oberholzer, A.E., Kiyani, W., Krojer, T., Shrestha, L., von Delft, F., Froese, D.S., Chaikuad, A., Raynor, J., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.14 kDa 
• Atom Count: 2,186 
• Modeled Residue Count: 225 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SORTING NEXIN-24	A, B	129	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y343 (Homo sapiens) Explore Q9Y343  Go to UniProtKB:  Q9Y343
PHAROS:  Q9Y343 GTEx:  ENSG00000064652

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.526	α = 90
b = 54.241	β = 90
c = 122.66	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Oberholzer, A.E., Kiyani, W., Krojer, T., Shrestha, L., von Delft, F., Froese, D.S., Chaikuad, A., Raynor, J., Arrowsmith, C., Edwards, A., Bountra, C., Yue, W.W.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Structure summary
• Version 1.2: 2013-11-20
  Changes: Derived calculations, Structure summary
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary