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- PDB-4r7m: Structure of the m17 leucyl aminopeptidase from malaria complexed... -

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Basic information

Entry
Database: PDB / ID: 4r7m
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 / identical protein binding / metal ion 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 / 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
Chem-3MW / CARBONATE ION / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 28, 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)714,48280
Polymers704,50812
Non-polymers9,97468
Water3,927218
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)357,46340
Polymers352,2546
Non-polymers5,20934
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31550 Å2
ΔGint-333 kcal/mol
Surface area96320 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)357,01940
Polymers352,2546
Non-polymers4,76534
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31080 Å2
ΔGint-461 kcal/mol
Surface area95850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.560, 175.590, 225.480
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 / Fragment: unp residues 84-605 / Mutation: D152N, D515N, D516N
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, 286 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-3MW / 4-amino-N-{(1R)-2-(hydroxyamino)-2-oxo-1-[4-(1H-pyrazol-1-yl)phenyl]ethyl}benzamide


Mass: 351.359 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C18H17N5O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#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.: 218 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
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: Mar 6, 2014
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: 2.85→36.01 Å / Num. obs: 144105 / % possible obs: 91.2 % / Redundancy: 2.4 % / Biso Wilson estimate: 23.14 Å2 / Rmerge(I) obs: 0.229 / Net I/σ(I): 3.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.85-2.92.20.6761.3194.1
15.35-36.012.60.0665.3176.4

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Processing

Software
NameVersionClassificationNB
Aimless0.2.4data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
GDAdata collection
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 2.85→36.01 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 31.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2909 7249 5.03 %
Rwork0.2375 --
obs0.2401 144000 90.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.71 Å2
Refinement stepCycle: LAST / Resolution: 2.85→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46712 0 535 218 47465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348162
X-RAY DIFFRACTIONf_angle_d0.68565336
X-RAY DIFFRACTIONf_dihedral_angle_d11.04617151
X-RAY DIFFRACTIONf_chiral_restr0.0287510
X-RAY DIFFRACTIONf_plane_restr0.0038283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.88240.3722430.32894694X-RAY DIFFRACTION94
2.8824-2.91630.36152580.32484676X-RAY DIFFRACTION94
2.9163-2.95180.35372580.32714662X-RAY DIFFRACTION93
2.9518-2.98920.37432460.324645X-RAY DIFFRACTION93
2.9892-3.02850.39342570.31444602X-RAY DIFFRACTION92
3.0285-3.070.35182420.31714624X-RAY DIFFRACTION93
3.07-3.11380.35032800.30564625X-RAY DIFFRACTION92
3.1138-3.16020.35382230.29724634X-RAY DIFFRACTION92
3.1602-3.20960.35452310.28934639X-RAY DIFFRACTION92
3.2096-3.26220.37282480.29864569X-RAY DIFFRACTION91
3.2622-3.31840.34152200.28714568X-RAY DIFFRACTION90
3.3184-3.37870.34152240.2774458X-RAY DIFFRACTION88
3.3787-3.44360.33392240.27594294X-RAY DIFFRACTION86
3.4436-3.51390.32752340.26534281X-RAY DIFFRACTION85
3.5139-3.59020.3062320.25174596X-RAY DIFFRACTION91
3.5902-3.67360.33952420.25164651X-RAY DIFFRACTION92
3.6736-3.76540.27952480.22844612X-RAY DIFFRACTION92
3.7654-3.86710.27992330.21724635X-RAY DIFFRACTION92
3.8671-3.98080.26632340.2154604X-RAY DIFFRACTION91
3.9808-4.10910.23732350.19444628X-RAY DIFFRACTION91
4.1091-4.25570.24292620.18084568X-RAY DIFFRACTION91
4.2557-4.42580.25122390.17254569X-RAY DIFFRACTION91
4.4258-4.62680.19612550.1694584X-RAY DIFFRACTION90
4.6268-4.87020.22242540.16754528X-RAY DIFFRACTION90
4.8702-5.17450.25152350.17854552X-RAY DIFFRACTION89
5.1745-5.57270.22742250.19744548X-RAY DIFFRACTION89
5.5727-6.13110.24962360.2064488X-RAY DIFFRACTION88
6.1311-7.01250.25882600.21184445X-RAY DIFFRACTION87
7.0125-8.81360.21972390.17564429X-RAY DIFFRACTION85
8.8136-36.01290.21382320.19124343X-RAY DIFFRACTION81
Refinement TLS params.Method: refined / Origin x: 88.7015 Å / Origin y: 55.7103 Å / Origin z: 78.3365 Å
111213212223313233
T0.164 Å20.0174 Å20.0277 Å2-0.1115 Å20.0307 Å2--0.2384 Å2
L0.0095 °2-0.0273 °20.0002 °2-0.0202 °20.0113 °2--0.0636 °2
S-0.0012 Å °0.0197 Å °-0.2149 Å °0.1317 Å °0.0052 Å °-0.0411 Å °0.0244 Å °-0.0011 Å °0.015 Å °
Refinement TLS groupSelection details: all

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