7AHF | pdb_00007ahf

Dimeric structure of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S L114E varaiant

• PDB DOI: https://doi.org/10.2210/pdb7AHF/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-09-24 Released: 2021-10-06 
• Deposition Author(s): Liess, A.K.L., Feiler, C.G., Lorenz, S.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Structural analyses of the ubiquitin-conjugating enzyme UBE2S in different crystal forms

Liess, A.K.L., Feiler, C.G., Lorenz, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: cross-linking

Macromolecule Content 

• Total Structure Weight: 35.15 kDa 
• Atom Count: 2,463 
• Modeled Residue Count: 297 
• Deposited Residue Count: 312 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 S	A [auth B], B [auth A]	156	Homo sapiens	Mutation(s): 1  Gene Names: UBE2S, E2EPF, OK/SW-cl.73 EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for Q16763 (Homo sapiens) Explore Q16763  Go to UniProtKB:  Q16763
PHAROS:  Q16763 GTEx:  ENSG00000108106

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth B], E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.317	α = 90
b = 48.411	β = 107.07
c = 70.127	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-10-06 
Deposition Author(s): Liess, A.K.L., Feiler, C.G., Lorenz, S.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	Emmy Noether LO 2003/1-1

Revision History  

• Version 1.0: 2021-10-06
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary