3M51

Structure of the 14-3-3/PMA2 complex stabilized by Pyrrolidone1

PDB DOI: https://doi.org/10.2210/pdb3M51/pdb

Classification: PROTEIN BINDING
Organism(s): Nicotiana tabacum, Nicotiana plumbaginifolia
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-03-12 Released: 2010-05-26
Deposition Author(s): Ottmann, C., Rose, R., Waldmann, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.340
R-Value Work: 0.310
R-Value Observed: 0.312

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Identification and structure of small-molecule stabilizers of 14-3-3 protein-protein interactions

Rose, R., Erdmann, S., Bovens, S., Wolf, A., Rose, M., Hennig, S., Waldmann, H., Ottmann, C.

(2010) Angew Chem Int Ed Engl 49: 4129-4132

PubMed: 20437433 Search on PubMed
DOI: https://doi.org/10.1002/anie.200907203
Primary Citation of Related Structures:
3M50, 3M51

Organizational Affiliation

Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227 Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 31.23 kDa
Atom Count: 2,052
Modelled Residue Count: 250
Deposited Residue Count: 271
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3-like protein C	A	240	Nicotiana tabacum	Mutation(s): 0
UniProt
Find proteins for P93343 (Nicotiana tabacum) Explore P93343 Go to UniProtKB: P93343
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P93343
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N.plumbaginifolia H+-translocating ATPase mRNA	B [auth P]	31	Nicotiana plumbaginifolia	Mutation(s): 3
UniProt
Find proteins for Q42932 (Nicotiana plumbaginifolia) Explore Q42932 Go to UniProtKB: Q42932
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q42932
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YR1 Query on YR1 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-hydroxy-5-[(5S)-3-hydroxy-5-(4-nitrophenyl)-2-oxo-4-(phenylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]benzoic acid C₂₄ H₁₆ N₂ O₈ SHWIONPIUOUFNT-FQEVSTJZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.340
R-Value Work: 0.310
R-Value Observed: 0.312
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.44	α = 90
b = 97.44	β = 90
c = 214.27	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-03-05
Changes: Database references
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.