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Basic information

Entry
Database: PDB / ID: 7ajr
TitleVirtual screening approach leading to the identification of a novel and tractable series of Pseudomonas aeruginosa elastase inhibitors
ComponentsKeratinase KP2
KeywordsHYDROLASE / Pseudomonas aeruginosa / elastase / inhibitors
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-RJB / Neutral metalloproteinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLeiris, S. / Davies, D.T. / Sprinsky, N. / Castandet, J. / Behria, L. / Bodnarchuk, M.S. / Sutton, J.M. / Mullins, T.M.G. / Jones, M.W. / Forrest, A.K. ...Leiris, S. / Davies, D.T. / Sprinsky, N. / Castandet, J. / Behria, L. / Bodnarchuk, M.S. / Sutton, J.M. / Mullins, T.M.G. / Jones, M.W. / Forrest, A.K. / Pallin, T.D. / Karunakar, P. / Martha, S.K. / Parusharamulu, B. / Ramula, R. / Kotha, V. / Pottabathini, N. / Pothukanuri, S. / Lemonnier, M. / Everett, M.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Virtual Screening Approach to Identifying a Novel and Tractable Series of Pseudomonas aeruginosa Elastase Inhibitors.
Authors: Leiris, S. / Davies, D.T. / Sprynski, N. / Castandet, J. / Beyria, L. / Bodnarchuk, M.S. / Sutton, J.M. / Mullins, T.M.G. / Jones, M.W. / Forrest, A.K. / Pallin, T.D. / Karunakar, P. / ...Authors: Leiris, S. / Davies, D.T. / Sprynski, N. / Castandet, J. / Beyria, L. / Bodnarchuk, M.S. / Sutton, J.M. / Mullins, T.M.G. / Jones, M.W. / Forrest, A.K. / Pallin, T.D. / Karunakar, P. / Martha, S.K. / Parusharamulu, B. / Ramula, R. / Kotha, V. / Pottabathini, N. / Pothukanuri, S. / Lemonnier, M. / Everett, M.
History
DepositionSep 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: 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 / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Keratinase KP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7034
Polymers33,1761
Non-polymers5283
Water2,414134
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area11730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.122, 51.260, 120.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Keratinase KP2


Mass: 33175.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Elastase domain / Source: (natural) Pseudomonas aeruginosa (bacteria)
References: UniProt: E3ULB4, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-RJB / 2-[2-(1,3-benzothiazol-2-ylmethylcarbamoyl)-1,3-dihydroinden-2-yl]ethanoic acid


Mass: 366.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18N2O3S / 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MOPS pH 6.5 and 1.5M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97717 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97717 Å / Relative weight: 1
ReflectionResolution: 1.75→47.226 Å / Num. obs: 28269 / % possible obs: 99.5 % / Redundancy: 6.2 % / CC1/2: 0.996 / Net I/σ(I): 11.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.2 % / Num. unique obs: 1500 / CC1/2: 0.591 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZM

1ezm


Resolution: 1.75→47.226 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: FREE R-VALUE / ESU R: 0.142 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2399 1425 5.051 %
Rwork0.2083 26788 -
all0.21 --
obs-28213 99.254 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.698 Å2-0 Å2-0 Å2
2--0.276 Å2-0 Å2
3---0.422 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 32 134 2462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132400
X-RAY DIFFRACTIONr_bond_other_d0.0370.0172010
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.6283262
X-RAY DIFFRACTIONr_angle_other_deg2.4421.5694652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1055299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30122.03133
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.81752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87615337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6751513
X-RAY DIFFRACTIONr_chiral_restr0.070.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022806
X-RAY DIFFRACTIONr_gen_planes_other0.010.02569
X-RAY DIFFRACTIONr_nbd_refined0.2010.2536
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2160.21839
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21240
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.2998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2118
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2680.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1360.26
X-RAY DIFFRACTIONr_nbd_other0.1840.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.26
X-RAY DIFFRACTIONr_mcbond_it1.911.5971196
X-RAY DIFFRACTIONr_mcbond_other1.8771.5951195
X-RAY DIFFRACTIONr_mcangle_it2.72.41495
X-RAY DIFFRACTIONr_mcangle_other2.6992.4031496
X-RAY DIFFRACTIONr_scbond_it3.1841.9341204
X-RAY DIFFRACTIONr_scbond_other3.1821.9271201
X-RAY DIFFRACTIONr_scangle_it4.842.7791767
X-RAY DIFFRACTIONr_scangle_other4.842.7671762
X-RAY DIFFRACTIONr_lrange_it5.57519.8192849
X-RAY DIFFRACTIONr_lrange_other5.56919.7052837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.4761080.4761911X-RAY DIFFRACTION97.8672
1.795-1.8450.5361060.4931895X-RAY DIFFRACTION98.7173
1.845-1.8980.397980.3971833X-RAY DIFFRACTION99.2292
1.898-1.9560.379750.3391801X-RAY DIFFRACTION98.9974
1.956-2.0210.288930.2291739X-RAY DIFFRACTION99.1879
2.021-2.0920.234960.2151690X-RAY DIFFRACTION99.8881
2.092-2.170.264860.2191643X-RAY DIFFRACTION99.6542
2.17-2.2590.212770.2121589X-RAY DIFFRACTION99.7008
2.259-2.3590.186770.1861520X-RAY DIFFRACTION99.6879
2.359-2.4750.253790.1841460X-RAY DIFFRACTION99.7408
2.475-2.6080.214700.1761398X-RAY DIFFRACTION99.5929
2.608-2.7660.22730.1711294X-RAY DIFFRACTION99.6356
2.766-2.9570.213720.171246X-RAY DIFFRACTION99.6221
2.957-3.1940.235470.1671183X-RAY DIFFRACTION99.7567
3.194-3.4990.204620.151055X-RAY DIFFRACTION99.4657
3.499-3.9110.165640.148967X-RAY DIFFRACTION99.3256
3.911-4.5160.197550.167860X-RAY DIFFRACTION98.9189
4.516-5.5290.222350.18752X-RAY DIFFRACTION98.9937
5.529-7.810.266350.196587X-RAY DIFFRACTION99.52
7.81-47.2260.232170.216365X-RAY DIFFRACTION99.2208

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