8HQL

Crystal structure of mouse SNX25 PX domain

PDB DOI: https://doi.org/10.2210/pdb8HQL/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-13 Released: 2023-12-20
Deposition Author(s): Yu, Z., Xu, J., Liu, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.242
R-Value Work: 0.199
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of mouse SNX25 PX domain

Yu, Z., Xu, J., Liu, J.

To be published.

Macromolecule Content

Total Structure Weight: 79.86 kDa
Atom Count: 5,209
Modelled Residue Count: 601
Deposited Residue Count: 640
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-25	A, B, C, D, E	128	Mus musculus	Mutation(s): 0 Gene Names: Snx25
UniProt & NIH Common Fund Data Resources
Find proteins for Q3ZT31 (Mus musculus) Explore Q3ZT31 Go to UniProtKB: Q3ZT31
IMPC: MGI:2142610
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3ZT31
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PE (Subject of Investigation/LOI) Query on 1PE Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain F [auth A] SDF format, chain FA [auth D] SDF format, chain G [auth A] SDF format, chain GA [auth D] SDF format, chain H [auth A] SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain LA [auth E] SDF format, chain MA [auth E] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain W [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain LA [auth E] MOL2 format, chain MA [auth E] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain W [auth C]	EA [auth D] F [auth A] FA [auth D] G [auth A] GA [auth D] EA [auth D], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], LA [auth E], MA [auth E], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], W [auth C]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C] Interactions & Density Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain GA [auth D] Focus chain H [auth A] Focus chain HA [auth D] Focus chain I [auth A] Focus chain LA [auth E] Focus chain MA [auth E] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain W [auth C]
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain OA [auth E] SDF format, chain PA [auth E] SDF format, chain X [auth C] SDF format, chain Y [auth C] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain OA [auth E] MOL2 format, chain PA [auth E] MOL2 format, chain X [auth C] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C]	AA [auth C] BA [auth C] IA [auth D] J [auth A] K [auth A] AA [auth C], BA [auth C], IA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth E], OA [auth E], PA [auth E], X [auth C], Y [auth C], Z [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth E] Focus chain OA [auth E] Focus chain PA [auth E] Focus chain X [auth C] Focus chain Y [auth C] Focus chain Z [auth C]
ACY (Subject of Investigation/LOI) Query on ACY Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain KA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain KA [auth D]	DA [auth C], KA [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain DA [auth C] Focus chain KA [auth D] Interactions & Density Focus chain DA [auth C] Focus chain KA [auth D]
CL (Subject of Investigation/LOI) Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain JA [auth D] SDF format, chain O [auth A] SDF format, chain QA [auth E] SDF format, chain V [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain JA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain V [auth B]	CA [auth C], JA [auth D], O [auth A], QA [auth E], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth C] Focus chain JA [auth D] Focus chain O [auth A] Focus chain QA [auth E] Focus chain V [auth B] Interactions & Density Focus chain CA [auth C] Focus chain JA [auth D] Focus chain O [auth A] Focus chain QA [auth E] Focus chain V [auth B]