9SM8 | pdb_00009sm8

Zuzalysin zymogen pentamer E439A

PDB DOI: https://doi.org/10.2210/pdb9SM8/pdb
EM Map EMD-55028: EMDB EMDataResource

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

Deposited: 2025-09-05 Released: 2026-09-16
Deposition Author(s): Rodriguez-Banqueri, A., Madej, M., Eckhard, U., Potempa, J., Gomis Ruth, F.X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9SM8

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

Literature

Structure of Zuzalysin zymogen pentamer E439A at 3.59 Angstroms resolution

Rodriguez-Banqueri, A., Madej, M., Eckhard, U., Potempa, J., Gomis-Ruth, F.X.

To be published.

Macromolecule Content

Total Structure Weight: 486.04 kDa
Atom Count: 32,820
Modeled Residue Count: 4,090
Deposited Residue Count: 4,260
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc-dependent metalloprotease	A, B, C, D, E	852	Porphyromonas gingivalis	Mutation(s): 0 Gene Names: NY149_10785
UniProt
Find proteins for A0AAF0BD41 (Porphyromonas gingivalis) Explore A0AAF0BD41 Go to UniProtKB: A0AAF0BD41
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AAF0BD41
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth E] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth E] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D], N [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.59 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	2.0rc1_5617
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-16

Deposition Author(s):

Rodriguez-Banqueri, A.

Gomis Ruth, F.X.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-09-16
Type: Initial release

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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.