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

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Basic information

Entry
Database: PDB / ID: 8qke
TitlePvSub1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (MH-13)
Components
  • Peptidomimetic Inhibitor (MH-13)
  • 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: 1.504 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 (MH-13)
D: Peptidomimetic Inhibitor (MH-13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,68213
Polymers141,0284
Non-polymers6549
Water7,116395
1
A: subtilisin
C: Peptidomimetic Inhibitor (MH-13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9527
Polymers70,5142
Non-polymers4385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: subtilisin
D: Peptidomimetic Inhibitor (MH-13)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7306
Polymers70,5142
Non-polymers2164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.02, 54.71, 69.14
Angle α, β, γ (deg.)69.39, 78.52, 75.02
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 (MH-13)


Mass: 628.674 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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, 403 molecules

#3: 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.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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, sitting drop / 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.5→47.5 Å / Num. obs: 104683 / % possible obs: 94.2 % / Redundancy: 3.5 % / CC1/2: 0.99 / Net I/σ(I): 6.88
Reflection shellResolution: 1.5→1.59 Å / Rmerge(I) obs: 1.26 / Num. unique obs: 16065

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.504→21.65 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.084 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.081
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 5232 -RANDOM
Rwork0.2091 ---
obs0.2099 104647 94.4 %-
Displacement parametersBiso mean: 30.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.1666 Å2-3.6949 Å20.0011 Å2
2---3.5585 Å2-1.2435 Å2
3---3.3919 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.504→21.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 118 395 5697
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015407HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.957344HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1881SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes937HARMONIC5
X-RAY DIFFRACTIONt_it5407HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion724SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5246SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.64
X-RAY DIFFRACTIONt_other_torsion15.14
LS refinement shellResolution: 1.504→1.52 Å
RfactorNum. reflection% reflection
Rfree0.4238 105 -
Rwork0.3774 --
obs--66.09 %
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)
11.1750.1925-0.31380.74950.03380.5709-0.0216-0.01970.0508-0.01970.0561-0.04110.0508-0.0411-0.0346-0.0221-0.0349-0.0072-0.01250.0048-0.004531.6117-48.9246-50.7842
21.1571-0.0193-0.16331.01520.01830.1692-0.05320.18760.05950.18760.0218-0.01930.0595-0.01930.03140.0482-0.0299-0.0019-0.04550.0019-0.015329.2756-61.3662-37.6488
33.11813.87521.80997.80030.75072.86630.05280.5616-0.13620.56160.0633-0.3145-0.1362-0.3145-0.11610.05820.00640.06030.0762-0.0806-0.031824.9863-41.6277-26.7211
40.9279-0.2247-0.20750.87930.11110.6311-0.03740.1516-0.02630.15160.09120.0239-0.02630.0239-0.05380.0157-0.0199-0.0232-0.0391-0.02940.012133.2365-44.1931-34.9291
52.321-0.1498-0.9413-0.5041-0.34890.6084-0.02460.1156-0.10450.11560.00120.1136-0.10450.11360.0234-0.0133-0.0471-0.0283-0.0316-0.03110.078447.3912-40.1713-40.7351
6-2.1064-4.8904-0.16810.2419-3.38394.32680.05090.37440.18070.3744-0.0135-0.2940.1807-0.294-0.0373-0.0364-0.12-0.06410.13990.139-0.00794.6387-68.422214.7624
70.7821-0.0775-0.23991.10560.19070.17570.0969-0.1844-0.1291-0.1844-0.1396-0.1142-0.1291-0.11420.04280.02130.0178-0.01110.003-0.0021-0.06333.2877-52.5937-4.0137
80.4499-0.5702-1.43511.4263-0.79141.6403-0.03-0.5785-0.052-0.5785-0.1421-0.202-0.052-0.2020.17210.07480.0446-0.03040.0987-0.0968-0.07231.7349-69.1225-22.2427
90.5541-0.07770.00040.90970.15190.72460.0299-0.1464-0.0311-0.1464-0.1105-0.0384-0.0311-0.03840.0806-0.01190.00370.0088-0.0057-0.002-0.0096.6665-66.1892-8.9871
102.18680.63831.05150.18880.6520.68040.0381-0.1110.0567-0.111-0.02790.16270.05670.1627-0.0102-0.03090.00570.0168-0.00810.04150.066820.6363-70.0602-4.9032
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|467 }A461 - 467
4X-RAY DIFFRACTION4{ A|476 - A|575 }A476 - 575
5X-RAY DIFFRACTION5{ A|576 - A|617 }A576 - 617
6X-RAY DIFFRACTION6{ B|277 - B|280 }B277 - 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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