3GUC

Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb3GUC/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-03-29 Released: 2009-05-26 
• Deposition Author(s): Walker, J.R., Bacik, J.P., Li, Y., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP

Walker, J.R., Bacik, J.P., Li, Y., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 64.97 kDa 
• Atom Count: 3,682 
• Modelled Residue Count: 463 
• Deposited Residue Count: 584 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like modifier-activating enzyme 5	A, B	292	Homo sapiens	Mutation(s): 0  Gene Names: UBA5, UBE1DC1 EC: 2.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZZ9 (Homo sapiens) Explore Q9GZZ9  Go to UniProtKB:  Q9GZZ9
PHAROS:  Q9GZZ9 GTEx:  ENSG00000081307

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.394	α = 90
b = 77.394	β = 90
c = 205.892	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-26 
Deposition Author(s): Walker, J.R., Bacik, J.P., Li, Y., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-11-12
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description