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- PDB-4r6t: Structure of the m17 leucyl aminopeptidase from malaria complexed... -

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Basic information

Entry
Database: PDB / ID: 4r6t
TitleStructure of the m17 leucyl aminopeptidase from malaria complexed with a hydroxamic acid-based inhibitor
ComponentsM17 leucyl aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
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 / cytoplasm / cytosol
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 / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like ...Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / Chem-R5T / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDrinkwater, N. / Mcgowan, S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Two-Pronged Attack: Dual Inhibition of Plasmodium falciparum M1 and M17 Metalloaminopeptidases by a Novel Series of Hydroxamic Acid-Based Inhibitors.
Authors: Mistry, S.N. / Drinkwater, N. / Ruggeri, C. / Sivaraman, K.K. / Loganathan, S. / Fletcher, S. / Drag, M. / Paiardini, A. / Avery, V.M. / Scammells, P.J. / McGowan, S.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)717,839104
Polymers704,50812
Non-polymers13,33192
Water30,4631691
1
A: M17 leucyl aminopeptidase
B: M17 leucyl aminopeptidase
C: M17 leucyl aminopeptidase
D: M17 leucyl aminopeptidase
E: M17 leucyl aminopeptidase
F: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,40554
Polymers352,2546
Non-polymers7,15148
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36000 Å2
ΔGint-602 kcal/mol
Surface area96330 Å2
MethodPISA
2
G: M17 leucyl aminopeptidase
H: M17 leucyl aminopeptidase
I: M17 leucyl aminopeptidase
J: M17 leucyl aminopeptidase
K: M17 leucyl aminopeptidase
L: M17 leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)358,43450
Polymers352,2546
Non-polymers6,18044
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33740 Å2
ΔGint-587 kcal/mol
Surface area96390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.895, 175.933, 231.647
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsthe biological unit is a hexamer, there are 2 biological units in the asymmetric unit

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
M17 leucyl aminopeptidase


Mass: 58708.973 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: LAP, PF14_0439 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8IL11

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Non-polymers , 7 types, 1783 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CO3
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-R5T / tert-butyl {(1S)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}carbamate


Mass: 332.354 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H20N4O4
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1691 / Source method: isolated from a natural source / Formula: H2O

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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: 2.51 Å3/Da / Density % sol: 51.09 %
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, 1 mM TCEP, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2013
RadiationMonochromator: DOUBLE CRYSTAL SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→77.95 Å / Num. all: 494683 / Num. obs: 189586 / Redundancy: 2.6 % / Biso Wilson estimate: 30.195 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.15data extraction
GDAdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KR4

3kr4


Resolution: 2.6→46.702 Å / SU ML: 0.37 / σ(F): 1.34 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2693 9431 4.98 %
Rwork0.2111 --
obs0.214 189404 87.09 %
all-494683 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.0838 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46718 0 673 1691 49082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00248251
X-RAY DIFFRACTIONf_angle_d0.60165439
X-RAY DIFFRACTIONf_dihedral_angle_d11.41117224
X-RAY DIFFRACTIONf_chiral_restr0.0247522
X-RAY DIFFRACTIONf_plane_restr0.0028266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.62960.37293280.2786089X-RAY DIFFRACTION89
2.6296-2.66050.35043210.28366115X-RAY DIFFRACTION90
2.6605-2.69290.41343300.29056132X-RAY DIFFRACTION90
2.6929-2.7270.38022890.2866110X-RAY DIFFRACTION89
2.727-2.76290.35623200.27916105X-RAY DIFFRACTION89
2.7629-2.80070.35943350.27036070X-RAY DIFFRACTION89
2.8007-2.84080.33363180.2596066X-RAY DIFFRACTION89
2.8408-2.88310.37283250.25956042X-RAY DIFFRACTION88
2.8831-2.92820.33723200.26366054X-RAY DIFFRACTION89
2.9282-2.97620.32123150.2446060X-RAY DIFFRACTION88
2.9762-3.02750.33423180.24865989X-RAY DIFFRACTION88
3.0275-3.08250.32223250.25386029X-RAY DIFFRACTION88
3.0825-3.14180.32543510.26055976X-RAY DIFFRACTION88
3.1418-3.20590.31832900.2435984X-RAY DIFFRACTION87
3.2059-3.27560.30012900.24016032X-RAY DIFFRACTION88
3.2756-3.35180.28563220.2196015X-RAY DIFFRACTION87
3.3518-3.43560.2912980.21485994X-RAY DIFFRACTION87
3.4356-3.52850.2543070.21525971X-RAY DIFFRACTION87
3.5285-3.63230.26063150.20855922X-RAY DIFFRACTION86
3.6323-3.74940.24843190.19845878X-RAY DIFFRACTION86
3.7494-3.88340.25132870.18845909X-RAY DIFFRACTION86
3.8834-4.03880.22722910.17465847X-RAY DIFFRACTION84
4.0388-4.22250.2132870.16585796X-RAY DIFFRACTION84
4.2225-4.44490.20793190.15935821X-RAY DIFFRACTION84
4.4449-4.72320.20453180.15525795X-RAY DIFFRACTION84
4.7232-5.08750.21423160.15595997X-RAY DIFFRACTION87
5.0875-5.59870.2253000.18066099X-RAY DIFFRACTION87
5.5987-6.4070.25063280.2016084X-RAY DIFFRACTION87
6.407-8.06540.21943330.1886034X-RAY DIFFRACTION86
8.0654-46.70940.18173160.18375958X-RAY DIFFRACTION82
Refinement TLS params.Method: refined / Origin x: 89.122 Å / Origin y: 55.5939 Å / Origin z: 79.8555 Å
111213212223313233
T0.2415 Å20.0341 Å20.0003 Å2-0.3346 Å20.0268 Å2--0.4065 Å2
L0.0262 °20.0234 °20.0183 °2-0.0579 °20.0165 °2--0.0912 °2
S0.0007 Å °-0.0224 Å °-0.0821 Å °0.005 Å °0.0079 Å °-0.0573 Å °0.0095 Å °0.0245 Å °-0.0078 Å °
Refinement TLS groupSelection details: all

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