4AZ9

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.205
R-Value Work: 0.181
R-Value Observed: 0.182

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y343
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.205
R-Value Work: 0.181
R-Value Observed: 0.182
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-10-10

Deposition Author(s):

Oberholzer, A.E.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.