1X23 | pdb_00001x23

Crystal structure of ubch5c

• PDB DOI: https://doi.org/10.2210/pdb1X23/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-04-19 Released: 2005-05-03 
• Deposition Author(s): Nakanishi, M., Teshima, N., Mizushima, T., Murata, S., Tanaka, K., Yamane, T.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.282 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ubch5c

Nakanishi, M., Teshima, N., Mizushima, T., Murata, S., Tanaka, K., Yamane, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 69.96 kDa 
• Atom Count: 5,544 
• Modeled Residue Count: 611 
• Deposited Residue Count: 620 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D3	A, B, C, D	155	Homo sapiens	Mutation(s): 0  EC: 6.3.2.19 (PDB Primary Data), 2.3.2.24 (UniProt), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61077 (Homo sapiens) Explore P61077  Go to UniProtKB:  P61077
PHAROS:  P61077 GTEx:  ENSG00000109332

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.282 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.998	α = 90
b = 44.334	β = 93.36
c = 97.584	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-05-03 
Deposition Author(s): Nakanishi, M., Teshima, N., Mizushima, T., Murata, S., Tanaka, K., Yamane, T.

Revision History  

• Version 1.0: 2005-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary