2IYD | pdb_00002iyd

SENP1 covalent complex with SUMO-2

• PDB DOI: https://doi.org/10.2210/pdb2IYD/pdb

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


• Deposited: 2006-07-14 Released: 2006-08-08 
• Deposition Author(s): Dong, C., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.288 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.272 (Depositor), 0.249 (DCC) 
• R-Value Observed: 
  0.273 (Depositor) 

Literature

Senp1 Native Structure

Dong, C., Naismith, J.H.

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 36.26 kDa 
• Atom Count: 2,524 
• Modeled Residue Count: 305 
• Deposited Residue Count: 307 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENTRIN-SPECIFIC PROTEASE 1	A	226	Homo sapiens	Mutation(s): 0  EC: 3.4.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0U3 (Homo sapiens) Explore Q9P0U3  Go to UniProtKB:  Q9P0U3
PHAROS:  Q9P0U3 GTEx:  ENSG00000079387

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SMALL UBIQUITIN-RELATED MODIFIER 2	B	81	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61956 (Homo sapiens) Explore P61956  Go to UniProtKB:  P61956
PHAROS:  P61956 GTEx:  ENSG00000188612

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.288 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.272 (Depositor), 0.249 (DCC) 
• R-Value Observed: 0.273 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.376	α = 90
b = 143.376	β = 90
c = 71.886	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-08 
Deposition Author(s): Dong, C., Naismith, J.H.

Revision History  

• Version 1.0: 2006-08-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Other