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- PDB-8qkg: PvSub1 Catalytic Domain in Complex with Peptidomimetic Inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 8qkg
TitlePvSub1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (MAM-125)
Components
  • Peptidomimetic Inhibitor (MAM-125)
  • subtilisin
KeywordsHYDROLASE / Subtilisin / Alpha-ketoamides / SAR
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. ...SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.538 Å
AuthorsBatista, F.A. / Martinez, M. / Bouillon, A. / Mechaly, A. / Alzari, P.M. / Haouz, A. / Barale, J.C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-19-CE18-0010 France
CitationJournal: Eur.J.Med.Chem. / Year: 2024
Title: Insights from structure-activity relationships and the binding mode of peptidic alpha-ketoamide inhibitors of the malaria drug target subtilisin-like SUB1.
Authors: Legru, A. / Batista, F.A. / Puszko, A.K. / Bouillon, A. / Maurel, M. / Martinez, M. / Ejjoummany, A. / Ortega Varga, L. / Adler, P. / Mechaly, A. / Hadjadj, M. / Sosnowski, P. / Hopfgartner, ...Authors: Legru, A. / Batista, F.A. / Puszko, A.K. / Bouillon, A. / Maurel, M. / Martinez, M. / Ejjoummany, A. / Ortega Varga, L. / Adler, P. / Mechaly, A. / Hadjadj, M. / Sosnowski, P. / Hopfgartner, G. / Alzari, P.M. / Blondel, A. / Haouz, A. / Barale, J.C. / Hernandez, J.F.
History
DepositionSep 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.identifier_ORCID / _citation_author.name
Revision 2.0May 1, 2024Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: subtilisin
B: subtilisin
C: Peptidomimetic Inhibitor (MAM-125)
D: Peptidomimetic Inhibitor (MAM-125)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,56212
Polymers141,0044
Non-polymers5588
Water7,404411
1
A: subtilisin
C: Peptidomimetic Inhibitor (MAM-125)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8446
Polymers70,5022
Non-polymers3414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: subtilisin
D: Peptidomimetic Inhibitor (MAM-125)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7186
Polymers70,5022
Non-polymers2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.38, 55.16, 69.03
Angle α, β, γ (deg.)69.2, 78.3, 74.75
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide / Sugars , 3 types, 5 molecules ABCD

#1: Protein subtilisin


Mass: 69885.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Gene: sub1, PVC01_100035100, PVT01_100029100, PVW1_100050600
Production host: Drosophila melanogaster (fruit fly) / References: UniProt: E6Y8B9, subtilisin
#2: Protein/peptide Peptidomimetic Inhibitor (MAM-125)


Mass: 616.663 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 418 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O

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Details

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

Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.5 M LiSO4, 15% W/V PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.538→64.056 Å / Num. obs: 98435 / % possible obs: 94 % / Redundancy: 1.9 % / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 1.538→1.565 Å / Num. unique obs: 9163 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.538→30.75 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 4856 -RANDOM
Rwork0.1795 ---
obs0.1807 98417 94 %-
Displacement parametersBiso mean: 22.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.8274 Å2-1.0306 Å2-0.8477 Å2
2---2.8303 Å2-3.0824 Å2
3---2.0029 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.538→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5170 0 111 411 5692
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015382HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.017315HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1866SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes932HARMONIC5
X-RAY DIFFRACTIONt_it5382HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion722SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5225SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4
X-RAY DIFFRACTIONt_other_torsion14.51
LS refinement shellResolution: 1.54→1.55 Å
RfactorNum. reflection% reflection
Rfree0.269 94 -
Rwork0.2336 --
obs0.2352 1969 87.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.14230.1301-0.29170.6817-0.10210.3022-0.0252-0.06910.0271-0.06910.0341-0.04080.0271-0.0408-0.0089-0.0409-0.0088-0.0092-0.00070.0102-0.040431.8511-48.6524-50.9574
20.97030.091-0.06470.9277-0.1260.2942-0.01620.08660.08680.0866-0.0128-0.02550.0868-0.02550.029-0.014-0.00460.0077-0.02550.0077-0.038829.4636-61.0747-37.6688
33.18151.6902-0.30261.5979-1.57233.91650.02510.4363-0.15540.43630.0426-0.2471-0.1554-0.2471-0.06780.0110.0070.02160.0263-0.04430.014826.4858-43.077-27.4618
40.9203-0.0176-0.14260.7951-0.01190.7598-0.02370.1372-0.04850.13720.02580.0035-0.04850.0035-0.0021-0.0202-0.0042-0.0109-0.0357-0.0102-0.020633.4699-43.9247-34.9413
51.1601-0.0042-0.4494-0.1207-0.26840.81860.00630.0619-0.08930.06190.0110.1253-0.08930.1253-0.0172-0.0069-0.0244-0.0197-0.0015-0.00810.03747.6213-39.9272-40.6948
63.6931-0.0968-1.20720.7246-3.08285.48960.08820.4618-0.0490.4618-0.1201-0.2615-0.049-0.26150.0319-0.08-0.025-0.02380.07930.07910.03144.6815-70.185612.5282
70.8102-0.1457-0.15290.9297-0.18140.52720.0257-0.0652-0.0751-0.0652-0.0392-0.0149-0.0751-0.01490.0134-0.02980.0025-0.008-0.0080.0021-0.04733.2566-52.6403-4.1602
82.68671.25670.2672.96370.35871.74430.005-0.5080.176-0.508-0.0266-0.12290.176-0.12290.02160.09620.0285-0.02690.0838-0.0524-0.01722.3461-68.5393-22.5256
90.794-0.0813-0.04380.92190.07430.98260.0111-0.12410.0525-0.1241-0.05540.01270.05250.01270.0443-0.02780.01670.0048-0.01560.002-0.01836.6739-66.1344-9.3533
101.96970.08350.53780.01640.00650.63420.0309-0.07990.0571-0.0799-0.0290.13360.05710.1336-0.0019-0.00080.03080.02710.02350.02830.049820.6509-70.0463-5.3922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|277 - A|331 }A277 - 331
2X-RAY DIFFRACTION2{ A|332 - A|460 }A332 - 460
3X-RAY DIFFRACTION3{ A|461 - A|466 }A461 - 466
4X-RAY DIFFRACTION4{ A|476 - A|575 }A476 - 575
5X-RAY DIFFRACTION5{ A|576 - A|617 }A576 - 617
6X-RAY DIFFRACTION6{ B|276 - B|280 }B276 - 280
7X-RAY DIFFRACTION7{ B|281 - B|458 }B281 - 458
8X-RAY DIFFRACTION8{ B|459 - B|485 }B459 - 485
9X-RAY DIFFRACTION9{ B|486 - B|573 }B486 - 573
10X-RAY DIFFRACTION10{ B|574 - B|617 }B574 - 617

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