8ITP

Crystal structure of USP47 catalytic domain complex with ubiquitin

• PDB DOI: https://doi.org/10.2210/pdb8ITP/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens, Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-03-22 Released: 2024-03-27 
• Deposition Author(s): Kim, E.E., Shin, S.C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.246 
• R-Value Observed: 0.250 

Literature

Structural and functional characterization of USP47 reveals a hot spot for inhibitor design

Shin, S.C., Park, J., Kim, K.H., Yoon, J.M., Cho, J., Ha, B.H., Oh, Y., Choo, H., Song, E.J., Kim, E.E.

(2023) Commun Biol 6: 970

• DOI: https://doi.org/10.1038/s42003-023-05345-5

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: 132.42 kDa 
• Atom Count: 6,771 
• Modelled Residue Count: 834 
• Deposited Residue Count: 1,168 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A [auth C], C [auth A]	76	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 47	B [auth D], D [auth B]	508	Caenorhabditis elegans	Mutation(s): 1  Gene Names: CELE_T05H10.1, T05H10.1 EC: 3.4.19.12
UniProt
Find proteins for Q22240 (Caenorhabditis elegans) Explore Q22240  Go to UniProtKB:  Q22240

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	E [auth D], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.284 
• R-Value Work: 0.246 
• R-Value Observed: 0.250 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.957	α = 90
b = 93.399	β = 90
c = 217.762	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	refinement
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Kim, E.E., Shin, S.C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release