6YLU | pdb_00006ylu

14-3-3sigma in complex with BLNKpT152 phosphopeptide crystal structure

• PDB DOI: https://doi.org/10.2210/pdb6YLU/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-04-07 Released: 2020-12-02 
• Deposition Author(s): Soini, L., Leysen, S., Davis, J., Ottmann, C.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

Literature

14-3-3sigma in complex with BLNKpT152 phosphopeptide crystal structure

Soini, L., Leysen, S., Davis, J., Ottmann, C.

(2020) J Struct Biol 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 27.91 kDa 
• Atom Count: 2,448 
• Modeled Residue Count: 245 
• Deposited Residue Count: 248 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein sigma	A	236	Homo sapiens	Mutation(s): 0  Gene Names: SFN, HME1
UniProt & NIH Common Fund Data Resources
Find proteins for P31947 (Homo sapiens) Explore P31947  Go to UniProtKB:  P31947
PHAROS:  P31947 GTEx:  ENSG00000175793

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BLNKpT152	B	12	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WV28 (Homo sapiens) Explore Q8WV28  Go to UniProtKB:  Q8WV28
PHAROS:  Q8WV28 GTEx:  ENSG00000095585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	B	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.25	α = 90
b = 112.11	β = 90
c = 62.52	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-02 
Deposition Author(s): Soini, L., Leysen, S., Davis, J., Ottmann, C.

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Funding Organization	Location	Grant Number
European Commission	Netherlands	675179

Revision History  

• Version 1.0: 2020-12-02
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary