5XPK

Crystal structure of ubiquitin-k6mimic

PDB DOI: https://doi.org/10.2210/pdb5XPK/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2017-06-03 Released: 2017-07-19
Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.310
R-Value Work: 0.250
R-Value Observed: 0.254

wwPDB Validation 3D Report Full Report

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

Literature

Structure of ubiquitin-k6mimic at 2.27 Angstroms resolution.

Man, P., Shuai, G., Qian, Q., Lei, L.

To be published.

Macromolecule Content

Total Structure Weight: 17.16 kDa
Atom Count: 1,217
Modelled Residue Count: 152
Deposited Residue Count: 152
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A	76	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0CG47
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ubiquitin	B	76	Homo sapiens	Mutation(s): 0 Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47 Go to UniProtKB: P0CG47
PHAROS: P0CG47
Entity Groups
UniProt Group	P0CG47
Protein Feature View Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SLZ Query on SLZ	A	L-PEPTIDE LINKING	C₅ H₁₂ N₂ O₂ S		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.310
R-Value Work: 0.250
R-Value Observed: 0.254
Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.656	α = 90
b = 46.626	β = 91.47
c = 40.495	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-07-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-07-19
Type: Initial release

RCSB PDB Core Operations are 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.