5AEK

Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W

• PDB DOI: https://doi.org/10.2210/pdb5AEK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-12-23 Released: 2016-01-20 
• Deposition Author(s): Gallego, P., Grana-Montes, R., Espargaro, A., Castillo, V., Torrent, J., Lange, R., Papaleo, E., Lindorff-Larsend, K., Ventura, S., Reverter, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.326 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 

Literature

Stepping Back and Forward on Sumo Folding Evolution

Grana-Montes, R., Gallego, P., Espargaro, A., Castillo, V., Torrent, J., Lange, R., Reverter, D., Papaleo, E., Lindorff-Larsend, K., Ventura, S.

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)

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PQS (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PQS (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PQS (software)

Biological Assembly 7  

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

Biological assembly 7 assigned by authors and generated by PQS (software)

Biological Assembly 8  

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

Biological assembly 8 assigned by authors and generated by PQS (software)

Biological Assembly 9  

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

Biological assembly 9 assigned by authors and generated by PQS (software)

Biological Assembly 10  

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

Biological assembly 10 assigned by authors and generated by PQS (software)

Biological Assembly 11  

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

Biological assembly 11 assigned by authors and generated by PQS (software)

Biological Assembly 12  

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

Biological assembly 12 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 428.2 kDa 
• Atom Count: 29,972 
• Modelled Residue Count: 3,612 
• Deposited Residue Count: 3,624 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENTRIN-SPECIFIC PROTEASE 2	A, C, E, G, I, K, M, O, Q, S, U, W	224	Homo sapiens	Mutation(s): 1  EC: 3.4.22.68
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC62 (Homo sapiens) Explore Q9HC62  Go to UniProtKB:  Q9HC62
PHAROS:  Q9HC62 GTEx:  ENSG00000163904

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SMALL UBIQUITIN-RELATED MODIFIER 1	B, D, F, H, J, L, N, P, R, T, V, X	78	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens) Explore P63165  Go to UniProtKB:  P63165
PHAROS:  P63165 GTEx:  ENSG00000116030

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.326 
• R-Value Work: 0.257 
• R-Value Observed: 0.259 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.721	α = 90
b = 119.319	β = 89.67
c = 199.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XPS	data reduction
CCP4I	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Gallego, P., Grana-Montes, R., Espargaro, A., Castillo, V., Torrent, J., Lange, R., Papaleo, E., Lindorff-Larsend, K., Ventura, S., Reverter, D.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2019-05-22
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Other, Refinement description