4QN1 | pdb_00004qn1

Crystal Structure of a Functionally Uncharacterized Domain of E3 Ubiquitin Ligase SHPRH

• PDB DOI: https://doi.org/10.2210/pdb4QN1/pdb

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


• Deposited: 2014-06-17 Released: 2014-08-13 
• Deposition Author(s): Dong, A., Zhang, Q., Li, Y., Walker, J.R., Guan, X., 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: 2.48 Å
• R-Value Free: 
  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Crystal structure of a Function Uncharacterized Domain of E3 Ubiquitin Ligase SHPRH

Zhang, Q., Dong, A., Li, Y., Walker, J.R., Guan, X., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y.

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)

Macromolecule Content 

• Total Structure Weight: 49.14 kDa 
• Atom Count: 3,069 
• Modeled Residue Count: 372 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase SHPRH	A	420	Homo sapiens	Mutation(s): 0  Gene Names: SHPRH, KIAA2023 EC: 3.6.4 (UniProt), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q149N8 (Homo sapiens) Explore Q149N8  Go to UniProtKB:  Q149N8
PHAROS:  Q149N8 GTEx:  ENSG00000146414

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	D [auth A]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.257 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.624	α = 90
b = 130.624	β = 90
c = 129.571	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-13 
Deposition Author(s): Dong, A., Zhang, Q., Li, Y., Walker, J.R., Guan, X., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-08-13
  Type: Initial release
  
• Version 1.1: 2014-12-03
  Changes: Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary