3E95 | pdb_00003e95

Crystal Structure of the Plasmodium Falciparum ubiquitin conjugating enzyme complex, PfUBC13-PfUev1a

• PDB DOI: https://doi.org/10.2210/pdb3E95/pdb

• Classification: LIGASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-21 Released: 2008-09-30 
• Deposition Author(s): Wernimont, A.K., Lam, A., Ali, A., Brokx, S., Lin, Y.H., Zhao, Y., Lew, J., Ravichandran, M., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilkstrom, M., BOuntra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Qiu, W., Brand, V.B., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.258 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Literature

Crystal Structure of the Plasmodium Falciparum ubiquitin conjugating enzyme complex, PfUBC13-PfUev1a

Wernimont, A.K., Lam, A., Ali, A., Brokx, S., Lin, Y.H., Zhao, Y., Lew, J., Ravichandran, M., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilkstrom, M., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Qiu, W., Brand, V.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 52.67 kDa 
• Atom Count: 3,577 
• Modeled Residue Count: 431 
• Deposited Residue Count: 460 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carrier protein	A, B	151	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PFE1350c EC: 6.3.2 (PDB Primary Data), 6.3.2.19 (UniProt)
UniProt
Find proteins for Q8I3J4 (Plasmodium falciparum (isolate 3D7)) Explore Q8I3J4  Go to UniProtKB:  Q8I3J4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2	C	158	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: MAL3P2.20, PFC0255c EC: 6.3.2.19
UniProt
Find proteins for O97241 (Plasmodium falciparum (isolate 3D7)) Explore O97241  Go to UniProtKB:  O97241

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	D [auth B], E [auth B], F [auth B], G [auth B], H [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.258 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.856	α = 90
b = 154.856	β = 90
c = 81.36	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Wernimont, A.K., Lam, A., Ali, A., Brokx, S., Lin, Y.H., Zhao, Y., Lew, J., Ravichandran, M., Wasney, G., Vedadi, M., Kozieradzki, I., Schapira, M., Bochkarev, A., Wilkstrom, M., BOuntra, C., Arrowsmith, C.H., Edwards, A.M., Hui, R., Qiu, W., Brand, V.B., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-09-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-09-18
  Changes: Derived calculations
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary