4IKD | pdb_00004ikd

Crystal structure of SNX11 PX domain

• PDB DOI: https://doi.org/10.2210/pdb4IKD/pdb

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


• Deposited: 2012-12-26 Released: 2013-04-24 
• Deposition Author(s): Xu, J., Xu, T., Liu, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.237 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Structure of Sorting Nexin 11 (SNX11) Reveals a Novel Extended PX Domain (PXe Domain) Critical for the Inhibition of Sorting Nexin 10 (SNX10) Induced Vacuolation

Xu, J., Xu, T., Liu, 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)

Macromolecule Content 

• Total Structure Weight: 20.4 kDa 
• Atom Count: 1,431 
• Modeled Residue Count: 148 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting nexin-11	A	172	Homo sapiens	Mutation(s): 0  Gene Names: SNX11 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5W9 (Homo sapiens) Explore Q9Y5W9  Go to UniProtKB:  Q9Y5W9
PHAROS:  Q9Y5W9 GTEx:  ENSG00000002919

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A], C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.237 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.12	α = 90
b = 62.4	β = 90
c = 66.06	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Xu, J., Xu, T., Liu, J.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary