9SLB | pdb_00009slb

Zuzalysin active bi-pentamer

PDB DOI: https://doi.org/10.2210/pdb9SLB/pdb

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

Deposited: 2025-09-03 Released: 2026-09-16
Deposition Author(s): Rodriguez-Banqueri, A., Eckhard, U., Potempa, J., Gomis Ruth, F.X.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.296 (Depositor), 0.284 (DCC)
R-Value Work:
0.257 (Depositor), 0.257 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9SLB

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

Literature

Structure of Zuzalysin metallopeptidase bi-pentamer at 3.0 Angstroms resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 950.03 kDa
Atom Count: 63,321
Modeled Residue Count: 7,750
Deposited Residue Count: 8,280
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 A, B, C, D, E, F, G, H, I, J	828	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain ZA [auth J] SDF format, chain X [auth C] SDF format, chain WA [auth I] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain TA [auth H] SDF format, chain R [auth B] SDF format, chain QA [auth G] SDF format, chain PA [auth G] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth F] SDF format, chain M [auth A] SDF format, chain LA [auth F] SDF format, chain KA [auth F] SDF format, chain HA [auth E] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain EA [auth E] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain ZA [auth J] MOL2 format, chain X [auth C] MOL2 format, chain WA [auth I] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain TA [auth H] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain PA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain KA [auth F] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain ZA [auth J] mmCIF format, chain X [auth C] mmCIF format, chain WA [auth I] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain TA [auth H] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain PA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain KA [auth F] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] EA [auth E] FA [auth E] GA [auth E] AA [auth D], BA [auth D], EA [auth E], FA [auth E], GA [auth E], HA [auth E], KA [auth F], LA [auth F], M [auth A], MA [auth F], N [auth A], O [auth A], PA [auth G], QA [auth G], R [auth B], TA [auth H], V [auth C], W [auth C], WA [auth I], X [auth C], ZA [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain R [auth B] Focus chain TA [auth H] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth I] Focus chain X [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain M [auth A] Focus chain MA [auth F] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain R [auth B] Focus chain TA [auth H] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth I] Focus chain X [auth C] Focus chain ZA [auth J]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain YA [auth J] SDF format, chain VA [auth I] SDF format, chain U [auth C] SDF format, chain SA [auth H] SDF format, chain Q [auth B] SDF format, chain OA [auth G] SDF format, chain L [auth A] SDF format, chain JA [auth F] SDF format, chain DA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain YA [auth J] MOL2 format, chain VA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain SA [auth H] MOL2 format, chain Q [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain JA [auth F] MOL2 format, chain DA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain YA [auth J] mmCIF format, chain VA [auth I] mmCIF format, chain U [auth C] mmCIF format, chain SA [auth H] mmCIF format, chain Q [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain JA [auth F] mmCIF format, chain DA [auth E]	DA [auth E] JA [auth F] L [auth A] OA [auth G] Q [auth B] DA [auth E], JA [auth F], L [auth A], OA [auth G], Q [auth B], SA [auth H], U [auth C], VA [auth I], YA [auth J], Z [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain JA [auth F] Focus chain L [auth A] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain SA [auth H] Focus chain U [auth C] Focus chain VA [auth I] Focus chain YA [auth J] Focus chain Z [auth D] Interactions & Density Focus chain DA [auth E] Focus chain JA [auth F] Focus chain L [auth A] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain SA [auth H] Focus chain U [auth C] Focus chain VA [auth I] Focus chain YA [auth J] Focus chain Z [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain XA [auth J] SDF format, chain UA [auth I] SDF format, chain T [auth C] SDF format, chain RA [auth H] SDF format, chain P [auth B] SDF format, chain NA [auth G] SDF format, chain K [auth A] SDF format, chain IA [auth F] SDF format, chain CA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth J] MOL2 format, chain UA [auth I] MOL2 format, chain T [auth C] MOL2 format, chain RA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth J] mmCIF format, chain UA [auth I] mmCIF format, chain T [auth C] mmCIF format, chain RA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] IA [auth F] K [auth A] NA [auth G] P [auth B] CA [auth E], IA [auth F], K [auth A], NA [auth G], P [auth B], RA [auth H], T [auth C], UA [auth I], XA [auth J], Y [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain IA [auth F] Focus chain K [auth A] Focus chain NA [auth G] Focus chain P [auth B] Focus chain RA [auth H] Focus chain T [auth C] Focus chain UA [auth I] Focus chain XA [auth J] Focus chain Y [auth D] Interactions & Density Focus chain CA [auth E] Focus chain IA [auth F] Focus chain K [auth A] Focus chain NA [auth G] Focus chain P [auth B] Focus chain RA [auth H] Focus chain T [auth C] Focus chain UA [auth I] Focus chain XA [auth J] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.296 (Depositor), 0.284 (DCC)
R-Value Work: 0.257 (Depositor), 0.257 (DCC)
R-Value Observed: 0.257 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.8	α = 98.2
b = 129.4	β = 104.7
c = 188.5	γ = 115.1

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

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
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PDC2022-133344-I00

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.