4MVT | pdb_00004mvt

Crystal structure of SUMO E3 Ligase PIAS3

• PDB DOI: https://doi.org/10.2210/pdb4MVT/pdb

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


• Deposited: 2013-09-24 Released: 2013-10-16 
• Deposition Author(s): Dong, A., Hu, J., Li, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.270 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SUMO E3 Ligase PIAS3

Hu, J., Dong, a., Li, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 168.05 kDa 
• Atom Count: 7,900 
• Modeled Residue Count: 1,008 
• Deposited Residue Count: 1,496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 SUMO-protein ligase PIAS3	A, B, C, D	374	Homo sapiens	Mutation(s): 0  Gene Names: PIAS3 EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6X2 (Homo sapiens) Explore Q9Y6X2  Go to UniProtKB:  Q9Y6X2
PHAROS:  Q9Y6X2 GTEx:  ENSG00000131788

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], JA [auth D], Q [auth B], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	F [auth A], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth D], O [auth A], OA [auth D], P [auth A], PA [auth D], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.270 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.45	α = 83.08
b = 85.44	β = 86.57
c = 89.53	γ = 86.14

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JBluIce-EPICS	data collection
HKL-3000	data reduction
MOLREP	phasing
BUSTER	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Dong, A., Hu, J., Li, Y., Tempel, W., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description