6JB6 | pdb_00006jb6

Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution

• PDB DOI: https://doi.org/10.2210/pdb6JB6/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-01-25 Released: 2019-03-20 
• Deposition Author(s): Lee, J.-G., Youn, H.-S., Lee, Y., An, J.Y., Park, K.R., Kang, J.Y., Mun, S.A., Park, J., Park, T., Jin, M.W., Yang, J., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Literature

Crystal structure of Ub-conjugated Ube2K C92K&K97A mutant (isopeptide linkage), 2.7 A resolution

Lee, J.-G., Eom, S.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 31.38 kDa 
• Atom Count: 2,198 
• Modeled Residue Count: 277 
• Deposited Residue Count: 281 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	A [auth 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 GTEx:  ENSG00000170315

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 K	B [auth A]	205	Homo sapiens	Mutation(s): 2  Gene Names: UBE2K, HIP2, LIG EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61086 (Homo sapiens) Explore P61086  Go to UniProtKB:  P61086
PHAROS:  P61086 GTEx:  ENSG00000078140

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.284 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 145.798	α = 90
b = 38.2	β = 93.551
c = 56.18	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): Lee, J.-G., Youn, H.-S., Lee, Y., An, J.Y., Park, K.R., Kang, J.Y., Mun, S.A., Park, J., Park, T., Jin, M.W., Yang, J., Eom, S.H.

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references