3PPA | pdb_00003ppa

Structure of the Dusp-Ubl domains of Usp15

• PDB DOI: https://doi.org/10.2210/pdb3PPA/pdb

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


• Deposited: 2010-11-24 Released: 2011-01-19 
• Deposition Author(s): Walker, J.R., Asinas, A.E., Dong, A., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.262 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Starting Model: experimental

Literature

Structure of the Dusp-Ubl Domains of the Ubiquitin-Specific Protease 15

Walker, J.R., Asinas, A.E., Dong, A., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 27.9 kDa 
• Atom Count: 1,668 
• Modeled Residue Count: 209 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 15	A	237	Homo sapiens	Mutation(s): 0  Gene Names: KIAA0529, USP15 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4E8 (Homo sapiens) Explore Q9Y4E8  Go to UniProtKB:  Q9Y4E8
PHAROS:  Q9Y4E8 GTEx:  ENSG00000135655

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.262 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.17	α = 90
b = 74.17	β = 90
c = 194.52	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-19 
Deposition Author(s): Walker, J.R., Asinas, A.E., Dong, A., Weigelt, J., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description