3HPC

Crystal structure of SNX5-PX domain in P21 space group

• PDB DOI: https://doi.org/10.2210/pdb3HPC/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2009-06-03 Released: 2009-06-23 
• Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

Starting Model: experimental

Literature

The Phox domain of sorting nexin 5 lacks ptdins(3)p specificity and preferentially binds to ptdins(4,5)P2

Koharudin, L.M.I., Furey, W., Liu, H., Liu, Y.-J., Gronenborn, A.M.

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)

Macromolecule Content

• Total Structure Weight: 18.54 kDa 
• Atom Count: 1,562 
• Modelled Residue Count: 155 
• Deposited Residue Count: 161 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snx5 protein	A [auth X]	161	Rattus norvegicus	Mutation(s): 0  Gene Names: Snx5 Membrane Entity: Yes
UniProt
Find proteins for B1H267 (Rattus norvegicus) Explore B1H267  Go to UniProtKB:  B1H267

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.598	α = 90
b = 41.424	β = 92.98
c = 47.227	γ = 90

Software Package:

Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Koharudin, L.M.I., Furey, W., Gronenborn, A.M.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description