5ZN9 | pdb_00005zn9

Crystal structure of PX domain

PDB DOI: https://doi.org/10.2210/pdb5ZN9/pdb

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

Deposited: 2018-04-08 Released: 2019-04-10
Deposition Author(s): Li, Y., Zhu, Z., Li, F., Liao, S., Xu, C.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of PX domain

Li, Y., Zhu, Z., Li, F., Liao, S., Xu, C.

To be published.

Macromolecule Content

Total Structure Weight: 26.46 kDa
Atom Count: 1,842
Modeled Residue Count: 201
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sorting nexin-27	A, B	110	Homo sapiens	Mutation(s): 0 Gene Names: SNX27, KIAA0488, My014
UniProt & NIH Common Fund Data Resources
Find proteins for Q96L92 (Homo sapiens) Explore Q96L92 Go to UniProtKB: Q96L92
PHAROS: Q96L92 GTEx: ENSG00000143376
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96L92
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.334	α = 90
b = 47.707	β = 90
c = 47.832	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31570737
National Natural Science Foundation of China	China	31500601

Revision History (Full details and data files)

Version 1.0: 2019-04-10
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description

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.