4ZFT

Catalytic domain of Sst2 F403W mutant bound to ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb4ZFT/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe 972h-, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-04-21 Released: 2015-10-14 
• Deposition Author(s): Bueno, A.N.
• Funding Organization(s): National Institutes of Health/National Center for Research Resources (NIH/NCRR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Model: experimental

Literature

Structure of the catalytic domain of Sst2 mutant F403W bound to ubiquitin at 2.3 Angstroms

Bueno, A.N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.59 kDa 
• Atom Count: 4,161 
• Modelled Residue Count: 523 
• Deposited Residue Count: 556 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AMSH-like protease sst2	A, C	197	Schizosaccharomyces pombe 972h-	Mutation(s): 1  Gene Names: sst2, SPAC19B12.10 EC: 3.4.19
UniProt
Find proteins for Q9P371 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q9P371  Go to UniProtKB:  Q9P371

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B, D	81	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], J [auth C], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	G [auth A], H [auth B], I [auth B], L [auth C], M [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.235 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.82	α = 90
b = 89.397	β = 90
c = 117.822	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Bueno, A.N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Center for Research Resources (NIH/NCRR)	United States	1R01RR026273

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2017-08-23
  Changes: Data collection, Derived calculations
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description