8AH4 | pdb_00008ah4

Crystal Structure of the third PDZ domain of PSD-95 protein in the space group P3112 at pH 4.0

PDB DOI: https://doi.org/10.2210/pdb8AH4/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: 1.48 Å
R-Value Free:
0.231 (Depositor), 0.232 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8AH4

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: 67.25 kDa
Atom Count: 4,689
Modeled Residue Count: 565
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cDNA FLJ50577, highly similar to Discs large homolog 4	A, B, C, D, E A, B, C, D, E, F	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 L [auth F] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth F] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth F] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth C] K [auth D] G [auth A], H [auth A], I [auth B], J [auth C], K [auth D], L [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.48 Å
R-Value Free: 0.231 (Depositor), 0.232 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.698	α = 90
b = 61.698	β = 90
c = 228.702	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

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

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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.