3EVI

Crystal structure of the thioredoxin-fold domain of human phosducin-like protein 2

• PDB DOI: https://doi.org/10.2210/pdb3EVI/pdb

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


• Deposited: 2008-10-13 Released: 2009-03-03 
• Deposition Author(s): Lou, X., Bao, R., Zhou, C., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structure of the thioredoxin-fold domain of human phosducin-like protein 2

Lou, X., Bao, R., Zhou, C.Z., Chen, Y.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 67-70

• PubMed: 19193988 
• DOI: https://doi.org/10.1107/S1744309108037342
• Primary Citation of Related Structures:  
  3EVI


• PubMed Abstract: 
  

  Human phosducin-like protein 2 (hPDCL2) has been identified as belonging to subgroup II of the phosducin (Pdc) family. The members of this family share an N-terminal helix domain and a C-terminal thioredoxin-fold (Trx-fold) domain. The X-ray crystal structure of the Trx-fold domain of hPDCL2 was solved at 2.70 A resolution and resembled the Trx-fold domain of rat phosducin. Comparative structural analysis revealed the structural basis of their putative functional divergence.

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Organizational Affiliation: 

Institute of Protein Research, Tongji University, Shanghai 200092, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 27.27 kDa 
• Atom Count: 1,945 
• Modelled Residue Count: 236 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosducin-like protein 2	A, B	118	Homo sapiens	Mutation(s): 0  Gene Names: PDCL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4E4 (Homo sapiens) Explore Q8N4E4  Go to UniProtKB:  Q8N4E4
GTEx:  ENSG00000163440

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.276 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.594	α = 90
b = 44.594	β = 90
c = 141.971	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-03 
Deposition Author(s): Lou, X., Bao, R., Zhou, C., Chen, Y.

Revision History  

• Version 1.0: 2009-03-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description