5EGG | pdb_00005egg

Crystal structure of human ubiquitin-conjugating enzyme UBCH5C

• PDB DOI: https://doi.org/10.2210/pdb5EGG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-27 Released: 2016-11-02 
• Deposition Author(s): Zhu, L., Li, H., Wu, F., Zhu, J.
• Funding Organization(s): the National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.253 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of recombinant human ubiquitin-conjugating enzyme UbcH5c

Wu, F., Zhu, J., Li, H., Zhu, L.

(2017) Acta Pharm Sin B 7: 390-394

• PubMed: 28540177 
• DOI: https://doi.org/10.1016/j.apsb.2016.12.008
• Primary Citation Related Structures: 
  5EGG


• PubMed Abstract: 
  

  UbcH5c belongs to the ubiquitin-conjugating enzyme family and plays an important role in catalyzing ubiquitination during TNF- α --triggered NF- κ B activation. Therefore, UbcH5c is a potent therapeutic target for the treatment of inflammatory and autoimmune diseases induced by aberrant activation of NF- κ B. In this study, we established a stable expression system for recombinant UbcH5c and solved the crystal structure of UbcH5c belonging to space group P22 ₁ 2 ₁ with one molecule in the asymmetric unit. This study provides the basis for further study of UbcH5c including the design of UbcH5c inhibitors.

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Organizational Affiliation: 
• Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.78 kDa 
• Atom Count: 1,245 
• Modeled Residue Count: 148 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D3	A	156	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D3, UBC5C, UBCH5C EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P61077 (Homo sapiens) Explore P61077  Go to UniProtKB:  P61077
PHAROS:  P61077 GTEx:  ENSG00000109332

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.253 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.17	α = 90
b = 66.28	β = 90
c = 76.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
AUTOMAR	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Zhu, L., Li, H., Wu, F., Zhu, J.

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Funding Organization	Location	Grant Number
the National Natural Science Foundation of China	China	81302697

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2017-07-26
  Changes: Advisory, Database references, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Advisory, Data collection, Database references, Refinement description