4X3G | pdb_00004x3g

Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide

• PDB DOI: https://doi.org/10.2210/pdb4X3G/pdb

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


• Deposited: 2014-11-28 Released: 2014-12-31 
• Deposition Author(s): Walker, J.R., Dong, A., Zhang, Q., Huang, X., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free: 
  0.251 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide

Walker, J.R., Dong, A., Zhang, Q., Huang, X., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 46.59 kDa 
• Atom Count: 3,173 
• Modelled Residue Count: 399 
• Deposited Residue Count: 414 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase SIAH1	A, B	193	Homo sapiens	Mutation(s): 0  Gene Names: SIAH1, HUMSIAH EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IUQ4 (Homo sapiens) Explore Q8IUQ4  Go to UniProtKB:  Q8IUQ4
PHAROS:  Q8IUQ4 GTEx:  ENSG00000196470

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 19	C, D	14	Homo sapiens	Mutation(s): 0  EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O94966 (Homo sapiens) Explore O94966  Go to UniProtKB:  O94966
PHAROS:  O94966 GTEx:  ENSG00000172046

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.34 Å
• R-Value Free:  0.251 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.343	α = 90
b = 88.092	β = 103.24
c = 59.59	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Walker, J.R., Dong, A., Zhang, Q., Huang, X., Li, Y., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Tong, Y., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Structure summary
• Version 1.2: 2018-01-24
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description