7NE7 | pdb_00007ne7

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.234 (Depositor), 0.237 (DCC)
R-Value Work:
0.188 (Depositor), 0.195 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3VI58
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TCK Query on TCK Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A]	N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide C₁₄ H₂₁ Cl N₂ O₃ S RDFCSSHDJSZMTQ-ZDUSSCGKSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SPM Query on SPM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain D [auth A]	B [auth A] C [auth A] D [auth A] G [auth A] H [auth A] 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		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

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