5XY9 | pdb_00005xy9

Structure of the MST4 and 14-3-3 complex

• PDB DOI: https://doi.org/10.2210/pdb5XY9/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-07-06 Released: 2018-07-11 
• Deposition Author(s): Shi, Z.B., Zhou, Z.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structure of the MST4 and 14-3-3 complex

Shi, Z., Zhou, Z.

To be published.

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)

Macromolecule Content 

• Total Structure Weight: 64.41 kDa 
• Atom Count: 3,859 
• Modeled Residue Count: 482 
• Deposited Residue Count: 558 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta	A, B	267	Homo sapiens	Mutation(s): 0  Gene Names: YWHAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P63104 (Homo sapiens) Explore P63104  Go to UniProtKB:  P63104
PHAROS:  P63104 GTEx:  ENSG00000164924

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from Serine/threonine-protein kinase 26	C, D	12	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P289 (Homo sapiens) Explore Q9P289  Go to UniProtKB:  Q9P289
PHAROS:  Q9P289 GTEx:  ENSG00000134602

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	F [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.994	α = 90
b = 84.734	β = 90
c = 111.859	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-07-11 
Deposition Author(s): Shi, Z.B., Zhou, Z.C.

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary