3M50 | pdb_00003m50

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

PDB DOI: https://doi.org/10.2210/pdb3M50/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: 2.60 Å
R-Value Free:
0.324 (Depositor), 0.302 (DCC)
R-Value Work:
0.255 (Depositor), 0.248 (DCC)
R-Value Observed:
0.259 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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 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: 31.08 kDa
Atom Count: 2,131
Modeled Residue Count: 249
Deposited Residue Count: 271
Unique protein chains: 2

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P93343
Sequence Annotations Expand
Reference Sequence

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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 EC: 7.1.2.1
UniProt
Find proteins for Q42932 (Nicotiana plumbaginifolia) Explore Q42932 Go to UniProtKB: Q42932
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q42932
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EBT Query on EBT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-[(2R,3R)-3-amino-2-hydroxy-4-phenylbutanoyl]-L-leucine C₁₆ H₂₄ N₂ O₄ VGGGPCQERPFHOB-HZSPNIEDSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.324 (Depositor), 0.302 (DCC)
R-Value Work: 0.255 (Depositor), 0.248 (DCC)
R-Value Observed: 0.259 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.62	α = 90
b = 97.62	β = 90
c = 217.03	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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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

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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.