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- PDB-8svm: Plasmodium falciparum M17 aminopeptidase bound to MMV1557817 -

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Basic information

Entry
Database: PDB / ID: 8svm
TitlePlasmodium falciparum M17 aminopeptidase bound to MMV1557817
ComponentsLeucine aminopeptidase
KeywordsHYDROLASE / metallo-exopeptidase / protease inhibitor / malaria / Plasmodium / M17 aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Macro domain-like
Similarity search - Domain/homology
CARBONATE ION / : / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMcGowan, S. / Drinkwater, N.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1185354 Australia
CitationJournal: Mbio / Year: 2024
Title: Characterisation of a novel antimalarial agent targeting haemaglobin digestion that shows cross-species reactivity and excellent in vivo properties.
Authors: de Koning-Ward, T.F. / Drinkwater, N. / Edgar, R.C.S. / McGowan, S. / Scammells, P.J.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucine aminopeptidase
B: Leucine aminopeptidase
C: Leucine aminopeptidase
D: Leucine aminopeptidase
E: Leucine aminopeptidase
F: Leucine aminopeptidase
G: Leucine aminopeptidase
H: Leucine aminopeptidase
I: Leucine aminopeptidase
J: Leucine aminopeptidase
K: Leucine aminopeptidase
L: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)719,355100
Polymers704,50812
Non-polymers14,84788
Water54,6393033
1
A: Leucine aminopeptidase
B: Leucine aminopeptidase
C: Leucine aminopeptidase
D: Leucine aminopeptidase
E: Leucine aminopeptidase
F: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,91651
Polymers352,2546
Non-polymers7,66245
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34900 Å2
ΔGint-384 kcal/mol
Surface area96800 Å2
MethodPISA
2
G: Leucine aminopeptidase
H: Leucine aminopeptidase
I: Leucine aminopeptidase
J: Leucine aminopeptidase
K: Leucine aminopeptidase
L: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,43949
Polymers352,2546
Non-polymers7,18543
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34790 Å2
ΔGint-396 kcal/mol
Surface area96180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.204, 177.926, 229.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Leucine aminopeptidase / PfLAP / M17 leucyl aminopeptidase / PfA-M17 / PfM17LAP


Mass: 58708.973 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: LAP, PF3D7_1446200 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IL11, leucyl aminopeptidase, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases

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Non-polymers , 6 types, 3121 molecules

#2: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-WRC / N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-3,3-dimethylbutanamide


Mass: 394.388 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H21F3N2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3033 / 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

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 40% (v/v) PEG 400, 0.1 M Tris pH 8.5, 0.2 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→49 Å / Num. obs: 306939 / % possible obs: 97.6 % / Redundancy: 3 % / CC1/2: 0.931 / Rmerge(I) obs: 0.331 / Rpim(I) all: 0.223 / Rrim(I) all: 0.402 / Net I/σ(I): 3.9
Reflection shellResolution: 2.3→2.34 Å / % possible obs: 96.3 % / Redundancy: 2.9 % / Rmerge(I) obs: 2.129 / Num. measured all: 43972 / Num. unique obs: 14962 / CC1/2: 0.15 / Rpim(I) all: 1.483 / Rrim(I) all: 2.614 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→49 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2521 15066 4.96 %
Rwork0.2044 --
obs0.2068 304005 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47031 0 756 3033 50820
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00448700
X-RAY DIFFRACTIONf_angle_d0.66766028
X-RAY DIFFRACTIONf_dihedral_angle_d13.04817420
X-RAY DIFFRACTIONf_chiral_restr0.0337558
X-RAY DIFFRACTIONf_plane_restr0.0038350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.38214570.31829127X-RAY DIFFRACTION92
2.3261-2.35350.38075040.30799369X-RAY DIFFRACTION95
2.3535-2.38220.35774710.29189442X-RAY DIFFRACTION96
2.3822-2.41240.34324920.28629525X-RAY DIFFRACTION96
2.4124-2.44410.35215140.28429528X-RAY DIFFRACTION97
2.4441-2.47760.31555230.26579584X-RAY DIFFRACTION97
2.4776-2.5130.31945310.26219584X-RAY DIFFRACTION97
2.513-2.55050.31245340.25659625X-RAY DIFFRACTION98
2.5505-2.59030.32115320.25859695X-RAY DIFFRACTION98
2.5903-2.63280.29555100.25299715X-RAY DIFFRACTION98
2.6328-2.67820.31415150.25689812X-RAY DIFFRACTION98
2.6782-2.72690.30135300.25349688X-RAY DIFFRACTION98
2.7269-2.77930.31295230.24659764X-RAY DIFFRACTION98
2.7793-2.83610.31385100.22989773X-RAY DIFFRACTION98
2.8361-2.89770.30374620.22299837X-RAY DIFFRACTION98
2.8977-2.96510.26364860.21189800X-RAY DIFFRACTION98
2.9651-3.03930.25274800.20479737X-RAY DIFFRACTION98
3.0393-3.12140.27484990.21159823X-RAY DIFFRACTION98
3.1214-3.21330.28945280.21719736X-RAY DIFFRACTION98
3.2133-3.31690.25185410.20849746X-RAY DIFFRACTION98
3.3169-3.43550.25165080.19339705X-RAY DIFFRACTION98
3.4355-3.5730.21224670.17669790X-RAY DIFFRACTION97
3.573-3.73550.21014820.16679706X-RAY DIFFRACTION97
3.7355-3.93240.20594550.16349740X-RAY DIFFRACTION97
3.9324-4.17870.17914860.15489688X-RAY DIFFRACTION96
4.1787-4.50110.17835160.14759593X-RAY DIFFRACTION96
4.5011-4.95370.19654660.14359528X-RAY DIFFRACTION94
4.9537-5.66960.20365360.1659516X-RAY DIFFRACTION94
5.6696-7.13950.22164820.17969514X-RAY DIFFRACTION93
7.1395-490.17665260.17219249X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 176.5625 Å / Origin y: 234.4452 Å / Origin z: 194.2267 Å
111213212223313233
T0.1218 Å2-0.0015 Å2-0.0004 Å2-0.1267 Å20.0082 Å2--0.1542 Å2
L0.0168 °2-0.0066 °2-0.0061 °2-0.0221 °20.0053 °2--0.0939 °2
S-0 Å °-0.0053 Å °0.0013 Å °0.0011 Å °0.002 Å °-0.0098 Å °0.0052 Å °0.0026 Å °-0.0021 Å °
Refinement TLS groupSelection details: all

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