9T45 | pdb_00009t45

Crystal Structure of the NlpC/P60 Peptidase YkfC C200A Mutant from Bacillus subtilis with Bound Pentapeptide

PDB DOI: https://doi.org/10.2210/pdb9T45/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis subsp. subtilis str. 168, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-10-30 Released: 2026-11-11
Deposition Author(s): Voelpel, S.V., Reiter, O.M., Stehle, T.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.300 (Depositor), 0.300 (DCC)
R-Value Work:
0.242 (Depositor), 0.243 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of the NlpC/P60 Peptidase YkfC from Bacillus subtilis

Voelpel, S.V., Mayer, C., Stehle, T.

To be published.

Macromolecule Content

Total Structure Weight: 138.98 kDa
Atom Count: 9,643
Modeled Residue Count: 1,236
Deposited Residue Count: 1,236
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase	A, B, C, D	304	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 1 Gene Names: ykfC, BSU12990 EC: 3.4.14.13
UniProt
Find proteins for O35010 (Bacillus subtilis (strain 168)) Explore O35010 Go to UniProtKB: O35010
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35010
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentapeptide (ALA-DGL-LYS-DAL-DAL)	E, F, G, H	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain I [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A]	I [auth A] J [auth A] L [auth B] M [auth C] N [auth C] I [auth A], J [auth A], L [auth B], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D]