5X3N | pdb_00005x3n

Crystal structure of DiUb-K6

• PDB DOI: https://doi.org/10.2210/pdb5X3N/pdb

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


• Deposited: 2017-02-06 Released: 2017-04-12 
• Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.276 (Depositor), 0.277 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

Structure of p-Ub-S65-NH2 at 1.82 Angstroms resolution.

Man, P., Shuai, G., Qian, Q., Lei, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.86 kDa 
• Atom Count: 689 
• Modeled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	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 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.276 (Depositor), 0.277 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P -1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.048	α = 102.05
b = 26.278	β = 94.14
c = 46.193	γ = 99.63

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-12 
Deposition Author(s): Man, P., Shuai, G., Qian, Q., Lei, L.

Revision History  

• Version 1.0: 2017-04-12
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations