6NEK

Crystal structure of a consensus PDZ domain

PDB DOI: https://doi.org/10.2210/pdb6NEK/pdb

Classification: DE NOVO PROTEIN
Organism(s): synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-12-17 Released: 2019-12-25
Deposition Author(s): Sun, Y.J., Gakhar, L., Fuentes, E.J.
Funding Organization(s): American Heart Association

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.226
R-Value Work: 0.197
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

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

Literature

Consensus PDZ domain

Sun, Y.J., Sternke, M., Barrick, D., Fuentes, E.J.

To be published.

Macromolecule Content

Total Structure Weight: 9.94 kDa
Atom Count: 704
Modelled Residue Count: 86
Deposited Residue Count: 93
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Consensus PDZ domain	A	93	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	B [auth A], C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		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: 1.63 Å
R-Value Free: 0.226
R-Value Work: 0.197
R-Value Observed: 0.198
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.62	α = 90
b = 60.09	β = 90
c = 73.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
XDS	data reduction
pointless	data scaling
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

Funding Organization	Location	Grant Number
American Heart Association	United States	15GRNT25740021

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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 R01GM133198.