5D2D

Crystal structure of human 14-3-3 zeta in complex with CFTR R-domain peptide pS753-pS768

• PDB DOI: https://doi.org/10.2210/pdb5D2D/pdb

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


• Deposited: 2015-08-05 Released: 2016-03-16 
• Deposition Author(s): Stevers, L.M., Leysen, S.F.R., Ottmann, C.
• Funding Organization(s): NWO

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 56.72 kDa 
• Atom Count: 4,041 
• Modelled Residue Count: 474 
• Deposited Residue Count: 488 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta	A, B	230	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
Cystic fibrosis transmembrane conductance regulator	C	28	Homo sapiens	Mutation(s): 0  EC: 3.6.3.49
UniProt & NIH Common Fund Data Resources
Find proteins for P13569 (Homo sapiens) Explore P13569  Go to UniProtKB:  P13569
PHAROS:  P13569 GTEx:  ENSG00000001626

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	D, E	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	F [auth A], G [auth A], H [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	C	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	D, E	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.220 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.862	α = 90
b = 112.862	β = 90
c = 158.192	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Stevers, L.M., Leysen, S.F.R., Ottmann, C.

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Funding Organization	Location	Grant Number
NWO	Netherlands	--

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary