9FMA | pdb_00009fma

Structure of Porphyromonas gingivalis endopeptidase (PgPepO)

PDB DOI: https://doi.org/10.2210/pdb9FMA/pdb

Classification: HYDROLASE
Organism(s): Porphyromonas gingivalis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-05 Released: 2025-12-17
Deposition Author(s): Zak, K.M., Grudnik, P., Waligorska, I., Ksiazek, M.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free:
0.214 (Depositor), 0.215 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.188 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of Tannerella forsythia endopeptidase O (TfPepO)

Zak, K., Waligorska, I., Ksiazek, M.

To be published.

Macromolecule Content

Total Structure Weight: 76.77 kDa
Atom Count: 5,800
Modeled Residue Count: 652
Deposited Residue Count: 667
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endopeptidase PepO	A	667	Porphyromonas gingivalis	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7MXL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.76 Å
R-Value Free: 0.214 (Depositor), 0.215 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.222	α = 90
b = 93.222	β = 90
c = 182.506	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	UMO-2019/35/B/NZ1/03118
Polish National Science Centre	Poland	UMO-2018/31/N/NZ1/02891

Revision History (Full details and data files)

Version 1.0: 2025-12-17
Type: Initial release

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.