2DWZ

Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome

• PDB DOI: https://doi.org/10.2210/pdb2DWZ/pdb

• Classification: ONCOPROTEIN
• Organism(s): Mus musculus, Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-08-22 Released: 2007-08-28 
• Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.268 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 

Literature

Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome

Nakamura, Y., Nakano, K., Umehara, T., Tanaka, A., Padmanabhan, B., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70 kDa 
• Atom Count: 4,864 
• Modelled Residue Count: 598 
• Deposited Residue Count: 628 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 10	A, C	231	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q9Z2X2 (Mus musculus) Explore Q9Z2X2  Go to UniProtKB:  Q9Z2X2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S protease regulatory subunit 6B	B, D	83	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for Q63570 (Rattus norvegicus) Explore Q63570  Go to UniProtKB:  Q63570

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.268 
• R-Value Work: 0.194 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.991	α = 90
b = 92.319	β = 90
c = 167.191	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-28 
Deposition Author(s): Padmanabhan, B., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-08-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations