7NE7

oligopeptidase B from S. proteomaculans with modified hinge region in complex with N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb7NE7/pdb

• Classification: HYDROLASE
• Organism(s): Serratia proteamaculans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-02-03 Released: 2021-02-17 
• Deposition Author(s): Petrenko, D.E., Nikolaeva, A.Y., Lazarenko, V.A., Dorovatovskiy, P.V., Vlaskina, A.V., Mikhailova, A.G., Rakitina, T.V., Timofeev, V.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

The Crystal Structure of N alpha-p-tosyl-lysyl Chloromethylketone-Bound Oligopeptidase B from Serratia Proteamaculans Revealed a New Type of Inhibitor Binding

Timofeev, V.I., Petrenko, D.E., Agapova, Y.K., Vlaskina, A.V., Karlinsky, D.M., Mikhailova, A.G., Kuranova, I.P., Rakitina, T.V.

(2021) Crystals (Basel) 11

• DOI: https://doi.org/10.3390/cryst11111438

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 80.34 kDa 
• Atom Count: 6,017 
• Modelled Residue Count: 677 
• Deposited Residue Count: 677 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptidase B	A	677	Serratia proteamaculans	Mutation(s): 0  Gene Names: opdB
UniProt
Find proteins for B3VI58 (Serratia proteamaculans) Explore B3VI58  Go to UniProtKB:  B3VI58

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TCK	E [auth A], F [auth A]	N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide C14 H21 Cl N2 O3 S RDFCSSHDJSZMTQ-ZDUSSCGKSA-N
SPM	B [auth A], C [auth A], D [auth A], G [auth A], H [auth A], I [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000459 (TCK)	E [auth A], F [auth A]	Tosyl-L-lysine chloromethyl ketone	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.234 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.32	α = 90
b = 101.1	β = 90
c = 108.76	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Petrenko, D.E., Nikolaeva, A.Y., Lazarenko, V.A., Dorovatovskiy, P.V., Vlaskina, A.V., Mikhailova, A.G., Rakitina, T.V., Timofeev, V.I.

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2023-01-18
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description