3HPB

Crystal structure of SNX5-PX domain in P212121 space group

PDB DOI: https://doi.org/10.2210/pdb3HPB/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.284
R-Value Work: 0.236
R-Value Observed: 0.240

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 18.68 kDa
Atom Count: 1,410
Modelled Residue Count: 154
Deposited Residue Count: 161
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Snx5 protein	A	161	Rattus norvegicus	Mutation(s): 0 Gene Names: Snx5
UniProt
Find proteins for B1H267 (Rattus norvegicus) Explore B1H267 Go to UniProtKB: B1H267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B1H267
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.284
R-Value Work: 0.236
R-Value Observed: 0.240
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.957	α = 90
b = 75.874	β = 90
c = 77.512	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-06-23

Deposition Author(s):

Koharudin, L.M.I.

Gronenborn, A.M.

Revision History (Full details and data files)

Version 1.0: 2009-06-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description

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.