Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.67 kDa 
• Atom Count: 2519 
• Residue Count: 296 
• Unique protein chains: 2

6NXK

Ubiquitin binding variants

• DOI: 10.2210/pdb6NXK/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
• Mutation(s): No 


• Deposited: 2019-02-08 Released: 2020-01-15 
• Deposition Author(s): Miller, D.J., Watson, E.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

A Protein Engineering Approach for Uncovering Cryptic Ubiquitin-binding Sites: from a Ubiquitin-Variant Inhibitor of APC/C to K48 Chain Binding

Watson, E.R., Grace, C.R.R., Zhang, W., Miller, D.J., Davidson, I.F., Prabu, J.R., Yu, S., Bolhuis, D.L., Haselbach, D., Stark, H., Peters, J.-M., Brown, N.G., Sidhu, S.S., Schulman, B.A.

To be published.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-C	A, B	76	Homo sapiens	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
NIH Common Fund Data Resources
PHAROS  P0CG48

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 2	C, D	90	Homo sapiens	Mutation(s): 0  Gene Names: ANAPC2, APC2, KIAA1406
Find proteins for Q9UJX6 (Homo sapiens) Explore Q9UJX6  Go to UniProtKB:  Q9UJX6
NIH Common Fund Data Resources
PHAROS  Q9UJX6 GTEx  ENSG00000176248

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.893	α = 90
b = 63.368	β = 90
c = 100.135	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-02-08 
• Released Date: 2020-01-15 
Deposition Author(s): Miller, D.J., Watson, E.R.

Revision History 

• Version 1.0: 2020-01-15
  Type: Initial release