3PYC | pdb_00003pyc

Crystal structure of human SMURF1 C2 domain

• PDB DOI: https://doi.org/10.2210/pdb3PYC/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2010-12-13 Released: 2011-04-06 
• Deposition Author(s): Li, X., Li, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of human SMURF1 C2 domain

Li, X., Li, P.

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: 15.07 kDa 
• Atom Count: 1,113 
• Modeled Residue Count: 132 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase SMURF1	A	132	Homo sapiens	Mutation(s): 0  Gene Names: SMURF1, KIAA1625 EC: 2.3.2.26 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCE7 (Homo sapiens) Explore Q9HCE7  Go to UniProtKB:  Q9HCE7
PHAROS:  Q9HCE7 GTEx:  ENSG00000198742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.241 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.959	α = 90
b = 47.048	β = 90
c = 91.266	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Li, X., Li, P.

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations