5AEK | pdb_00005aek

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.326 (Depositor), 0.319 (DCC)
R-Value Work:
0.257 (Depositor), 0.255 (DCC)
R-Value Observed:
0.259 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SENTRIN-SPECIFIC PROTEASE 2	A, C, E, G, I A, C, E, G, I, K, M, O, Q, S, U, W	224	Homo sapiens	Mutation(s): 1 EC: 3.4.22.68 (PDB Primary Data), 3.4.22 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC62 (Homo sapiens) Explore Q9HC62 Go to UniProtKB: Q9HC62
PHAROS: Q9HC62 GTEx: ENSG00000163904
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HC62
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SMALL UBIQUITIN-RELATED MODIFIER 1	B, D, F, H, J 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63165
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.326 (Depositor), 0.319 (DCC)
R-Value Work: 0.257 (Depositor), 0.255 (DCC)
R-Value Observed: 0.259 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Grana-Montes, R.

Lindorff-Larsend, K.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.