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- PDB-9h0y: ProA in complex with inhibitor 7 -

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Basic information

Entry
Database: PDB / ID: 9h0y
TitleProA in complex with inhibitor 7
ComponentsZinc metalloproteinase
KeywordsHYDROLASE / ProA / Legionella pneumophila / inhibitor / 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
: / (R,R)-2,3-BUTANEDIOL / Zinc metalloproteinase
Similarity search - Component
Biological speciesLegionella pneumophila str. Corby (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc metalloproteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,21213
Polymers37,7891
Non-polymers1,42412
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-5 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.650, 56.510, 74.120
Angle α, β, γ (deg.)90.00, 96.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 306 molecules

#2: Chemical ChemComp-A1IRL / [(2~{R})-1-[[(2~{R})-1-[(3,4-dichlorophenyl)amino]-3-methyl-1-oxidanylidene-butan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]phosphonic acid


Mass: 439.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25Cl2N2O5P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: IndexHT condidion A5: 0.2 M (NH4)2SO4; 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03285 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03285 Å / Relative weight: 1
ReflectionResolution: 1.5→40.42 Å / Num. obs: 52208 / % possible obs: 98.8 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15
Reflection shellResolution: 1.5→1.533 Å / Rmerge(I) obs: 0.864 / Num. unique obs: 2562 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→40.42 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1656 2571 4.93 %
Rwork0.1575 --
obs0.1579 52195 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.51→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 86 294 2974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072788
X-RAY DIFFRACTIONf_angle_d1.1183769
X-RAY DIFFRACTIONf_dihedral_angle_d14.0581020
X-RAY DIFFRACTIONf_chiral_restr0.068375
X-RAY DIFFRACTIONf_plane_restr0.012492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.51-1.540.26071380.2532712X-RAY DIFFRACTION99
1.54-1.570.24711580.22972749X-RAY DIFFRACTION99
1.57-1.60.24451330.21422714X-RAY DIFFRACTION98
1.6-1.640.22241290.22648X-RAY DIFFRACTION95
1.64-1.680.20431450.19962735X-RAY DIFFRACTION99
1.68-1.730.25781470.2062789X-RAY DIFFRACTION100
1.73-1.780.16791320.19922767X-RAY DIFFRACTION100
1.78-1.830.20571510.1842797X-RAY DIFFRACTION100
1.83-1.90.19761420.17012748X-RAY DIFFRACTION100
1.9-1.980.16981480.16082780X-RAY DIFFRACTION100
1.98-2.060.16331420.16532749X-RAY DIFFRACTION100
2.06-2.170.19421520.1582729X-RAY DIFFRACTION98
2.17-2.310.14491550.15032671X-RAY DIFFRACTION96
2.31-2.490.1531480.14582788X-RAY DIFFRACTION100
2.49-2.740.15921310.14932814X-RAY DIFFRACTION100
2.74-3.130.16991520.1552814X-RAY DIFFRACTION100
3.14-3.950.11771520.13432758X-RAY DIFFRACTION99
3.95-40.420.15941160.14382862X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 14.243 Å / Origin y: -4.0005 Å / Origin z: 16.6502 Å
111213212223313233
T0.128 Å20.0029 Å20.0119 Å2-0.1133 Å20.0205 Å2--0.1215 Å2
L1.8347 °20.5445 °20.7541 °2-0.9017 °20.6441 °2--1.2836 °2
S-0.0704 Å °0.1365 Å °0.0712 Å °0.0147 Å °0.0672 Å °-0.012 Å °-0.018 Å °0.1414 Å °-0.0028 Å °
Refinement TLS groupSelection details: all

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