5HDY | pdb_00005hdy

The third PDZ domain from the synaptic protein PSD-95

PDB DOI: https://doi.org/10.2210/pdb5HDY/pdb

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

Deposited: 2016-01-05 Released: 2017-01-11
Deposition Author(s): White, K.I., Raman, A.S., Ranganathan, R.
Funding Organization(s): Robert A. Welch Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.220 (Depositor), 0.227 (DCC)
R-Value Work:
0.186 (Depositor), 0.190 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The third PDZ domain from the synaptic protein PSD-95

White, K.I., Raman, A.S., Ranganathan, R.

To be published.

Macromolecule Content

Total Structure Weight: 12.83 kDa
Atom Count: 1,223
Modeled Residue Count: 117
Deposited Residue Count: 119
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large homolog 4	A	119	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
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.220 (Depositor), 0.227 (DCC)
R-Value Work: 0.186 (Depositor), 0.190 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.657	α = 90
b = 89.657	β = 90
c = 89.657	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-01-11

Deposition Author(s):

Ranganathan, R.

Funding Organization	Location	Grant Number
Robert A. Welch Foundation	United States	I-1366

Revision History (Full details and data files)

Version 1.0: 2017-01-11
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, 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.