9UDJ | pdb_00009udj

Crystal structure of PSD95 in complex with 4-dimethylaminophenol

PDB DOI: https://doi.org/10.2210/pdb9UDJ/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-04-07 Released: 2026-04-15
Deposition Author(s): Li, H., Ouyang, Q., Zhu, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.274 (Depositor), 0.276 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of PSD95 in complex with 4-dimethylaminophenol

Li, H., Ouyang, Q., Zhu, J.

To be published.

Macromolecule Content

Total Structure Weight: 41.89 kDa
Atom Count: 2,985
Modeled Residue Count: 362
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large homolog 4	A, B	181	Rattus norvegicus	Mutation(s): 0 Gene Names: Dlg4, Dlgh4, Psd95
UniProt
Find proteins for P31016 (Rattus norvegicus) Explore P31016 Go to UniProtKB: P31016
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P31016
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EOW (Subject of Investigation/LOI) Query on A1EOW Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	4-(dimethylamino)phenol C₈ H₁₁ N O JVVRCYWZTJLJSG-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.274 (Depositor), 0.276 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.54	α = 90
b = 90.442	β = 102.59
c = 55.947	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82090041
National Natural Science Foundation of China (NSFC)	China	32470728
National Natural Science Foundation of China (NSFC)	China	82001265

Revision History (Full details and data files)

Version 1.0: 2026-04-15
Type: Initial release

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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.