7OD0 | pdb_00007od0

Mirolysin in complex with compound 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.204 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7OD0

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Latency, thermal stability, and identification of an inhibitory compound of mirolysin, a secretory protease of the human periodontopathogen Tannerella forsythia .

Zak, K.M.Bostock, M.J.Waligorska, I.Thogersen, I.B.Enghild, J.J.Popowicz, G.M.Grudnik, P.Potempa, J.Ksiazek, M.

(2021) J Enzyme Inhib Med Chem 36: 1267-1281

  • DOI: https://doi.org/10.1080/14756366.2021.1937619
  • Primary Citation Related Structures: 
    7OD0

  • PubMed Abstract: 

    Mirolysin is a secretory protease of Tannerella forsythia , a member of the dysbiotic oral microbiota responsible for periodontitis. In this study, we show that mirolysin latency is achieved by a "cysteine-switch" mechanism exerted by Cys23 in the N-terminal profragment. Mutation of Cys23 shortened the time needed for activation of the zymogen from several days to 5 min. The mutation also decreased the thermal stability and autoproteolysis resistance of promirolysin. Mature mirolysin is a thermophilic enzyme and shows optimal activity at 65 °C. Through NMR-based fragment screening, we identified a small molecule (compound (cpd) 9 ) that blocks promirolysin maturation and functions as a competitive inhibitor ( K i = 3.2 µM), binding to the S1' subsite of the substrate-binding pocket. Cpd 9 shows superior specificity and does not interact with other T. forsythia proteases or Lys/Arg-specific proteases.


  • Organizational Affiliation
    • Helmholtz Zentrum München, Institute of Structural Biology, Neuherberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 188.81 kDa 
  • Atom Count: 14,240 
  • Modeled Residue Count: 1,612 
  • Deposited Residue Count: 1,662 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mirolysin277Tannerella forsythiaMutation(s): 0 
UniProt
Find proteins for A0A0F7IPS1 (Tannerella forsythia)
Explore A0A0F7IPS1 
Go to UniProtKB:  A0A0F7IPS1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F7IPS1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V7Q
(Subject of Investigation/LOI)

Query on V7Q



Download:Ideal Coordinates CCD File
G [auth AAA]
HA [auth EEE]
M [auth BBB]
OA [auth FFF]
S [auth CCC]
G [auth AAA],
HA [auth EEE],
M [auth BBB],
OA [auth FFF],
S [auth CCC],
Z [auth DDD]
2,1,3-benzothiadiazol-4-ylmethanamine
C7 H7 N3 S
HMEXAOROCQLCJX-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
EA [auth DDD]
J [auth AAA]
LA [auth EEE]
P [auth BBB]
SA [auth FFF]
EA [auth DDD],
J [auth AAA],
LA [auth EEE],
P [auth BBB],
SA [auth FFF],
U [auth CCC]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
CA [auth DDD]
DA [auth DDD]
H [auth AAA]
IA [auth EEE]
JA [auth EEE]
CA [auth DDD],
DA [auth DDD],
H [auth AAA],
IA [auth EEE],
JA [auth EEE],
N [auth BBB],
PA [auth FFF],
QA [auth FFF]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
AA [auth DDD]
BA [auth DDD]
I [auth AAA]
KA [auth EEE]
O [auth BBB]
AA [auth DDD],
BA [auth DDD],
I [auth AAA],
KA [auth EEE],
O [auth BBB],
RA [auth FFF],
T [auth CCC]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
FA [auth DDD]
GA [auth DDD]
K [auth AAA]
L [auth AAA]
MA [auth EEE]
FA [auth DDD],
GA [auth DDD],
K [auth AAA],
L [auth AAA],
MA [auth EEE],
NA [auth EEE],
Q [auth BBB],
R [auth BBB],
TA [auth FFF],
UA [auth FFF],
V [auth CCC],
VA [auth FFF],
W [auth CCC],
X [auth CCC]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
Y [auth CCC]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.593α = 92.462
b = 77.64β = 90
c = 81.995γ = 119.98
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2019/35/B/NZ1/03118
Polish National Science CentrePolandUMO-2018/31/N/NZ1/02891

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary