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- PDB-8coy: Structure of the catalytic domain of P. vivax Sub1 (triclinic cry... -

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Basic information

Entry
Database: PDB / ID: 8coy
TitleStructure of the catalytic domain of P. vivax Sub1 (triclinic crystal form) in complex with inhibitor
Components
  • peptido-mimetic inhibitor
  • subtilisin
KeywordsHYDROLASE / Plasmodium / serine protease / drug target / malaria / pseudo-peptide inhibitor
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: 1.507 Å
AuthorsMartinez, M. / Bouillon, A. / Batista, F. / Alzari, P.M. / Barale, J.C. / Haouz, A.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: 3D structures of the Plasmodium vivax subtilisin-like drug target SUB1 reveal conformational changes to accommodate a substrate-derived alpha-ketoamide inhibitor.
Authors: Martinez, M. / Batista, F.A. / Maurel, M. / Bouillon, A. / Ortega Varga, L. / Wehenkel, A.M. / Le Chevalier-Sontag, L. / Blondel, A. / Haouz, A. / Hernandez, J.F. / Alzari, P.M. / Barale, J.C.
History
DepositionMar 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 22, 2023Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_ec / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: subtilisin
B: subtilisin
C: peptido-mimetic inhibitor
D: peptido-mimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,26414
Polymers77,3894
Non-polymers87510
Water8,827490
1
A: subtilisin
C: peptido-mimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1327
Polymers38,6952
Non-polymers4385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: subtilisin
D: peptido-mimetic inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1327
Polymers38,6952
Non-polymers4385
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.260, 55.100, 69.010
Angle α, β, γ (deg.)69.22, 78.31, 74.76
Int Tables number1
Space group name H-MP1

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD

#1: Protein subtilisin


Mass: 38003.852 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) / Strain (production host): Schneider 2 / References: UniProt: E6Y8B9, subtilisin
#2: Protein/peptide peptido-mimetic inhibitor


Mass: 690.698 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The sequence of chains D,E is: ACE-Ile-Thr-Ala-VEF-Asp-Glu, where VEF is: (3~{S})-3-AZANYL-2-OXIDANYLIDENE-BUTANOIC ACID and is covalently linked to Ser549 of chains A,B respectively: LINK ...Details: The sequence of chains D,E is: ACE-Ile-Thr-Ala-VEF-Asp-Glu, where VEF is: (3~{S})-3-AZANYL-2-OXIDANYLIDENE-BUTANOIC ACID and is covalently linked to Ser549 of chains A,B respectively: LINK OG SER A 549 C2 VEF D 4 1.430 LINK OG SER B 549 C2 VEF E 4 1.430
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.: 2 / 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, 498 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: isolated from a natural source / 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.: 490 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.67 %
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: 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: 1.507→64 Å / Num. obs: 104444 / % possible obs: 94.1 % / Redundancy: 1.9 % / CC1/2: 1 / Rpim(I) all: 0.031 / Net I/σ(I): 12
Reflection shellResolution: 1.51→1.53 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5196 / CC1/2: 0.78 / Rpim(I) all: 0.337 / % possible all: 92.8

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.507→29.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.073 / SU Rfree Blow DPI: 0.07 / SU Rfree Cruickshank DPI: 0.07
RfactorNum. reflection% reflectionSelection details
Rfree0.1922 5074 4.86 %RANDOM
Rwork0.1764 ---
obs0.1771 104436 94.1 %-
Displacement parametersBiso mean: 23.83 Å2
Baniso -1Baniso -2Baniso -3
1-1.7913 Å2-0.7344 Å2-1.3161 Å2
2---2.819 Å2-1.3606 Å2
3---1.0277 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 1.507→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 64 490 5798
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0165427HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.067367HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1865SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes945HARMONIC5
X-RAY DIFFRACTIONt_it5427HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.33
X-RAY DIFFRACTIONt_other_torsion14.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion730SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5383SEMIHARMONIC4
LS refinement shellResolution: 1.51→1.52 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2077 106 5.07 %
Rwork0.2397 1983 -
all0.2381 2089 -
obs--93.31 %
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)
10.81170.1475-0.10560.6819-0.05590.406-0.0042-0.02640.04660.1056-0.0003-0.02730.0123-0.00560.0046-0.03310.0008-0.0094-0.03540.0067-0.042733.189-50.668-39.2
20.7647-0.2373-0.16170.9407-0.09440.42640.0510.0506-0.0577-0.1528-0.0907-0.0616-0.00910.01210.0397-0.0350.01410.0008-0.010.013-0.05646.205-59.74-6.692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|277 - A|903 }A277 - 903
2X-RAY DIFFRACTION2{ B|276 - B|903 }B276 - 903

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