8AH5

Crystal Structure of the third PDZ domain of PSD-95 protein in the space group P212121 at pH 4.6

PDB DOI: https://doi.org/10.2210/pdb8AH5/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-20 Released: 2023-03-08
Deposition Author(s): Camara-Artigas, A., Salinas Garcia, M.C.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.185
R-Value Work: 0.148
R-Value Observed: 0.149

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

pH-Driven Polymorphic Behaviour of the Third PDZ Domain of PSD95: The Role of Electrostatic Interactions

Salinas-Garcia, M.C., Plaza-Garrido, M., Gavira, J.A., Murciano-Calles, J., Andujar-Sanchez, M., Ortiz-Salmeron, E., Martinez, J.C., Camara-Artigas, A.

(2023) Crystals (Basel)

DOI: https://doi.org/10.3390/cryst13020218

Macromolecule Content

Total Structure Weight: 11.27 kDa
Atom Count: 1,004
Modelled Residue Count: 102
Deposited Residue Count: 104
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cDNA FLJ50577, highly similar to Discs large homolog 4	A	104	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P78352 (Homo sapiens) Explore P78352 Go to UniProtKB: P78352
PHAROS: P78352 GTEx: ENSG00000132535
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P78352
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.185
R-Value Work: 0.148
R-Value Observed: 0.149
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.845	α = 90
b = 32.344	β = 90
c = 88.305	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Camara-Artigas, A.

Salinas Garcia, M.C.

Funding Organization	Location	Grant Number
Other government	Spain	UAL-FEDER-UAL18-BIO-B005-B

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 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.