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- PDB-7qh1: Discovery and development of a novel inhaled antivirulence therap... -

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Basic information

Entry
Database: PDB / ID: 7qh1
TitleDiscovery and development of a novel inhaled antivirulence therapy for the treatment of Pseudomonas aeruginosa infections in patients with chronic respiratory disease
ComponentsKeratinase KP2
KeywordsHYDROLASE / Pseudomonas aeruginosa / respiratory disease
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
PepSY domain / Peptidase propeptide and YPEB domain / : / 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
Similarity search - Domain/homology
Chem-CI8 / Neutral metalloproteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsLeonard, P.M. / Davies, D. / Pallin, T.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Infect Dis. / Year: 2023
Title: Chemical Optimization of Selective Pseudomonas aeruginosa LasB Elastase Inhibitors and Their Impact on LasB-Mediated Activation of IL-1 beta in Cellular and Animal Infection Models.
Authors: Everett, M.J. / Davies, D.T. / Leiris, S. / Sprynski, N. / Llanos, A. / Castandet, J.M. / Lozano, C. / LaRock, C.N. / LaRock, D.L. / Corsica, G. / Docquier, J.D. / Pallin, T.D. / Cridland, A. ...Authors: Everett, M.J. / Davies, D.T. / Leiris, S. / Sprynski, N. / Llanos, A. / Castandet, J.M. / Lozano, C. / LaRock, C.N. / LaRock, D.L. / Corsica, G. / Docquier, J.D. / Pallin, T.D. / Cridland, A. / Blench, T. / Zalacain, M. / Lemonnier, M.
History
DepositionDec 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Keratinase KP2
B: Keratinase KP2
C: Keratinase KP2
D: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,71920
Polymers132,7024
Non-polymers3,01716
Water50428
1
A: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9305
Polymers33,1761
Non-polymers7544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9305
Polymers33,1761
Non-polymers7544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9305
Polymers33,1761
Non-polymers7544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9305
Polymers33,1761
Non-polymers7544
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.980, 44.520, 161.710
Angle α, β, γ (deg.)90.00, 100.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Keratinase KP2


Mass: 33175.531 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria)
References: UniProt: E3ULB4, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CI8 / 2-[2-[[5-[3-[bis(2-hydroxyethyl)-methyl-$l^{4}-azanyl]propoxy]-6-methoxy-1,3-benzothiazol-2-yl]methylcarbamoyl]-5,6-bis(fluoranyl)-1,3-dihydroinden-2-yl]ethanoic acid


Mass: 608.674 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H36F2N3O7S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.23 Å3/Da / Density % sol: 61.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MOPS pH 6.5, 1.3-1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.74→41.69 Å / Num. obs: 44296 / % possible obs: 97.2 % / Redundancy: 3.1 % / CC1/2: 0.917 / Net I/σ(I): 3.9
Reflection shellResolution: 2.74→2.81 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3215 / CC1/2: 0.305

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DBK

3dbk


Resolution: 2.74→41.73 Å / Cor.coef. Fo:Fc: 0.88 / Cor.coef. Fo:Fc free: 0.828 / SU B: 22.916 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R: 1.128 / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30117 2143 4.8 %RANDOM
Rwork0.2561 ---
obs0.25825 42147 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.263 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20.23 Å2
2--0.83 Å20 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.74→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9268 0 180 28 9476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0139801
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178288
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.64913317
X-RAY DIFFRACTIONr_angle_other_deg1.2591.57919201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25351210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.65521.786560
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.995151411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8861564
X-RAY DIFFRACTIONr_chiral_restr0.0620.21187
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211442
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022334
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2153.734819
X-RAY DIFFRACTIONr_mcbond_other2.2153.734818
X-RAY DIFFRACTIONr_mcangle_it3.5415.5946036
X-RAY DIFFRACTIONr_mcangle_other3.5415.5946037
X-RAY DIFFRACTIONr_scbond_it2.4063.9114982
X-RAY DIFFRACTIONr_scbond_other2.4063.9124983
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.895.7947282
X-RAY DIFFRACTIONr_long_range_B_refined7.32670.68742111
X-RAY DIFFRACTIONr_long_range_B_other7.32470.69842102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.74→2.811 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 179 -
Rwork0.376 3030 -
obs--96.31 %

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