5XDP | pdb_00005xdp

K11/48-branched teraubiquitin

• PDB DOI: https://doi.org/10.2210/pdb5XDP/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2017-03-28 Released: 2017-04-19 
• Deposition Author(s): Liang, L., Gao, S., Tang, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 
  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

K11/48-branched teraubiquitin

Liang, L., Gao, S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.13 kDa 
• Atom Count: 1,239 
• Modeled Residue Count: 148 
• Deposited Residue Count: 152 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ubiquitin	A [auth B]	76	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin-B	B [auth A]	76	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.938	α = 103.03
b = 26.163	β = 94.16
c = 46.54	γ = 99.65

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-19 
Deposition Author(s): Liang, L., Gao, S., Tang, S.

Revision History  

• Version 1.0: 2017-04-19
  Type: Initial release
  
• Version 1.1: 2022-02-09
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Refinement description