7Z0J

human PEX13 SH3 domain in complex with internal FxxxF motif

PDB DOI: https://doi.org/10.2210/pdb7Z0J/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-23 Released: 2023-03-08
Deposition Author(s): Gaussmann, S., Zak, K., Kreisz, N., Sattler, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228
R-Value Work: 0.185
R-Value Observed: 0.188

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Intramolecular autoinhibition of human PEX13 modulates peroxisomal import

Gaussmann, S., Ott, J., Zak, K.M., Delhommel, F., Popowicz, G.M., Schliebs, W., Erdmann, R., Sattler, M.

(2022) Biorxiv

DOI: https://doi.org/10.1101/2022.12.19.520972

Macromolecule Content

Total Structure Weight: 23.33 kDa
Atom Count: 1,413
Modelled Residue Count: 170
Deposited Residue Count: 218
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal membrane protein PEX13	A, B	109	Homo sapiens	Mutation(s): 0 Gene Names: PEX13
UniProt & NIH Common Fund Data Resources
Find proteins for Q92968 (Homo sapiens) Explore Q92968 Go to UniProtKB: Q92968
PHAROS: Q92968 GTEx: ENSG00000162928
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92968
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 B] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B]	C [auth A], D [auth B], E [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228
R-Value Work: 0.185
R-Value Observed: 0.188
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.808	α = 90
b = 86.808	β = 90
c = 65.436	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	FOR1905

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, 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.