Macromolecule Content

Total Structure Weight: 37672.98
Atom Count: 2403
Residue Count: 332
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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.2 Å
R-Value Free: 0.266
R-Value Work: 0.221

wwPDB Validation3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-C	A, B	76	Homo sapiens	Mutation(s): 0 Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens) Go to Gene View: UBC Go to UniProtKB: P0CG48
Protein Feature View Full Protein Feature View for P0CG48

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Anaphase-promoting complex subunit 2	C, D	90	Homo sapiens	Mutation(s): 0 Gene Names: ANAPC2 (APC2, KIAA1406)
Find proteins for Q9UJX6 (Homo sapiens) Go to Gene View: ANAPC2 Go to UniProtKB: Q9UJX6
Protein Feature View Full Protein Feature View for Q9UJX6

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.2 Å
R-Value Free: 0.266
R-Value Work: 0.221
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 58.893	α = 90.00
b = 63.368	β = 90.00
c = 100.135	γ = 90.00

Software Package:

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

Structure Validation

View Full Validation Report or Ramachandran Plots

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.