1YF9 | pdb_00001yf9

Structural analysis of Leishmania major ubiquitin conjugating enzyme E2

• PDB DOI: https://doi.org/10.2210/pdb1YF9/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Leishmania major
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-31 Released: 2005-02-22 
• Deposition Author(s): Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Structural Analysis of Leishmania major ubiquitin conjugating enzyme E2

Bosch, J., Hol, W.G.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.69 kDa 
• Atom Count: 4,338 
• Modeled Residue Count: 477 
• Deposited Residue Count: 513 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carrier protein 4	A, B, C	171	Leishmania major	Mutation(s): 0
UniProt
Find proteins for Q4Q5L3 (Leishmania major) Explore Q4Q5L3  Go to UniProtKB:  Q4Q5L3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.448	α = 90
b = 114.448	β = 90
c = 139.547	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations, Refinement description