9KN2 | pdb_00009kn2

Crystallization of zinc metalloproteinase PepO from Porphyromonas gingivalis

• PDB DOI: https://doi.org/10.2210/pdb9KN2/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Porphyromonas gingivalis W83
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-11-18 Released: 2025-10-01 
• Deposition Author(s): Feng, C.Y., Feng, C.Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 
  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: in silico

Literature

Structural and biochemical characterization of a zinc metallopeptidase from Porphyromonas gingivalis.

Feng, C., Yu, W., Jiang, Y., Xia, R.

(2025) Biochem Biophys Res Commun 744: 151201-151201

• PubMed: 39709774 
• DOI: https://doi.org/10.1016/j.bbrc.2024.151201
• Primary Citation of Related Structures:  
  9KN2


• PubMed Abstract: 
  

  The pathogen Porphyromonas gingivalis contributes to the pathogenesis of periodontitis and other systemic diseases. The zinc-dependent metallopeptidase PepO is a virulence factor that plays a crucial role in the adhesion and invasion of Porphyromonas gingivalis to human cells. Here, we solved the 2.04 Å crystal structure of wild-type PepO in complex with the inhibitor phosphoramidon. The active-site pocket of PepO appears to exhibit an increased hydrophobicity and a more pronounced negative charge, highlighting distinct structural features compared to its homologs. In addition to phosphoramidon, several zinc metallopeptidase inhibitors, including thiorphan, omapatrilat, and sacubitrilat, exhibited varying degrees of inhibition on PepO enzymatic activity. Notably, the recombinant PepO showed distinct binding profiles to human fibrinogen, a characteristic that likely contributes to its role as virulence factors. These findings provide significant insights into the structural and functional mechanisms of PepO, offering a platform for the rational design of targeted inhibitors against the periodontal pathogen P. gingivalis.

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Organizational Affiliation: 
• Department of Stomatology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230601, PR China.
School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, PR China. Electronic address: [e-mail].
Department of Stomatology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230601, PR China. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 77.17 kDa 
• Atom Count: 6,274 
• Modeled Residue Count: 651 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endopeptidase PepO	A	664	Porphyromonas gingivalis W83	Mutation(s): 0  Gene Names: pepO, PG_0159
UniProt
Find proteins for Q7MXL5 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MXL5  Go to UniProtKB:  Q7MXL5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RDF (Subject of Investigation/LOI)	B [auth A]	N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN C23 H34 N3 O10 P ZPHBZEQOLSRPAK-XLCYBJAPSA-N
SO4 (Subject of Investigation/LOI)	D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN (Subject of Investigation/LOI)	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000638 (RDF)	B [auth A]	PHOSPHORAMIDON	Glycopeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free:  0.190 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.19	α = 90
b = 121.19	β = 90
c = 199.018	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MLPHARE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Feng, C.Y., Feng, C.Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release