[English] 日本語
Yorodumi
- PDB-9h0x: ProA in complex with inhibitor 6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h0x
TitleProA in complex with inhibitor 6
ComponentsZinc metalloproteinase
KeywordsHYDROLASE / inhibitor / ProA / Legionella pneumophila / antibiotics
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
: / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
: / Zinc metalloproteinase
Similarity search - Component
Biological speciesLegionella pneumophila str. Corby (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsOrnago, C. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Innovative zinc-binding inhibitors of Legionella pneumophila ProA reduce collagen and flagellin degradation, TLR5 evasion, and human lung tissue inflammation.
Authors: Scheithauer, L. / Ornago, C. / Selmar, J. / Schutz, C. / Bianchi, G. / Kiefer, A. / Haupenthal, J. / Dellmann, A. / Huynh, D. / Zhang, R. / Blankenfeldt, W. / Hirsch, A.H. / Steinert, M.
History
DepositionOct 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3353
Polymers37,7891
Non-polymers5462
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.914, 74.950, 76.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Zinc metalloproteinase / PEP1 / PRO A


Mass: 37788.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila str. Corby (bacteria)
Production host: Legionella pneumophila str. Corby (bacteria)
References: UniProt: P21347, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-A1IRK / (2~{R})-2-(2-methylpropyl)-~{N}-[4-[[4-[(2-methylpropylsulfonylamino)methyl]-1,2,3-triazol-1-yl]methyl]phenyl]-~{N}'-oxidanyl-propanediamide


Mass: 480.581 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H32N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JSCG+ condition F16: 0.1 M HEPES pH 7, 30% Jeff-M-600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 1.36→47.08 Å / Num. obs: 72913 / % possible obs: 99.2 % / Redundancy: 10.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.025 / Rrim(I) all: 0.083 / Χ2: 0.86 / Net I/σ(I): 14.7 / Num. measured all: 776332
Reflection shellResolution: 1.36→1.44 Å / % possible obs: 99.2 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.853 / Num. measured all: 113983 / Num. unique obs: 10514 / CC1/2: 0.863 / Rpim(I) all: 0.266 / Rrim(I) all: 0.895 / Χ2: 0.64 / Net I/σ(I) obs: 2.6

-
Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→47.08 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1656 3518 4.83 %
Rwork0.1484 --
obs0.1493 72837 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2603 0 34 402 3039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162780
X-RAY DIFFRACTIONf_angle_d1.4483772
X-RAY DIFFRACTIONf_dihedral_angle_d12.9431044
X-RAY DIFFRACTIONf_chiral_restr0.101370
X-RAY DIFFRACTIONf_plane_restr0.017507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.25391380.22672732X-RAY DIFFRACTION99
1.38-1.40.23351250.21682741X-RAY DIFFRACTION99
1.4-1.420.21451330.20882768X-RAY DIFFRACTION99
1.42-1.450.24111350.19672727X-RAY DIFFRACTION99
1.45-1.470.20061310.1892746X-RAY DIFFRACTION99
1.47-1.50.20451250.17452774X-RAY DIFFRACTION99
1.5-1.520.18121470.17182736X-RAY DIFFRACTION100
1.52-1.550.18861470.16572750X-RAY DIFFRACTION99
1.55-1.580.18521230.15542750X-RAY DIFFRACTION99
1.58-1.620.17861170.15152755X-RAY DIFFRACTION98
1.62-1.660.17661390.1492718X-RAY DIFFRACTION98
1.66-1.70.18021510.14912762X-RAY DIFFRACTION99
1.7-1.740.16231260.14422755X-RAY DIFFRACTION99
1.74-1.790.16041370.14392752X-RAY DIFFRACTION99
1.79-1.850.18621660.14752757X-RAY DIFFRACTION100
1.85-1.920.1491460.14922776X-RAY DIFFRACTION99
1.92-1.990.15881350.14532787X-RAY DIFFRACTION100
1.99-2.090.16031500.14242774X-RAY DIFFRACTION100
2.09-2.20.17551470.13532741X-RAY DIFFRACTION98
2.2-2.330.1521220.13752782X-RAY DIFFRACTION98
2.33-2.510.15171380.13572815X-RAY DIFFRACTION99
2.51-2.770.17931740.14872783X-RAY DIFFRACTION100
2.77-3.170.16011620.15292820X-RAY DIFFRACTION99
3.17-3.990.14061590.13452849X-RAY DIFFRACTION99
3.99-47.080.16361450.14872969X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -13.9156 Å / Origin y: 14.4324 Å / Origin z: -17.237 Å
111213212223313233
T0.1133 Å2-0.0097 Å2-0.01 Å2-0.0878 Å20.0036 Å2--0.1105 Å2
L1.1473 °2-0.4787 °2-0.5174 °2-0.73 °20.2791 °2--1.3245 °2
S0.0284 Å °0.0629 Å °-0.0011 Å °-0.0675 Å °-0.0136 Å °-0.0332 Å °0.0248 Å °0.0125 Å °0.0092 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more