3HPC | pdb_00003hpc

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.234 (Depositor), 0.231 (DCC)
R-Value Work:
0.184 (Depositor), 0.180 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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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: 18.54 kDa
Atom Count: 1,562
Modeled Residue Count: 155
Deposited Residue Count: 161
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.234 (Depositor), 0.231 (DCC)
R-Value Work: 0.184 (Depositor), 0.180 (DCC)
R-Value Observed: 0.187 (Depositor)

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

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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: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.