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- PDB-6eee: X-ray crystal structure of Pf-M17 in complex with inhibitor (6k) ... -

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Basic information

Entry
Database: PDB / ID: 6eee
TitleX-ray crystal structure of Pf-M17 in complex with inhibitor (6k) and regulatory zinc ion
ComponentsM17 LEUCYL-AMINOPEPTIDASE
Keywordshydrolase/hydrolase inhibitor / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / proteolysis / 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
CARBONATE ION / Chem-J4V / leucyl aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDrinkwater, N. / McGowan, S.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1063786 Australia
Australian Research Council (ARC)FT100100690 Australia
CitationJournal: J. Med. Chem. / Year: 2019
Title: Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases.
Authors: Vinh, N.B. / Drinkwater, N. / Malcolm, T.R. / Kassiou, M. / Lucantoni, L. / Grin, P.M. / Butler, G.S. / Duffy, S. / Overall, C.M. / Avery, V.M. / Scammells, P.J. / McGowan, S.
History
DepositionAug 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_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)707,993123
Polymers690,77612
Non-polymers17,217111
Water39,6152199
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)352,97555
Polymers345,3886
Non-polymers7,58849
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36250 Å2
ΔGint-365 kcal/mol
Surface area95670 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)355,01868
Polymers345,3886
Non-polymers9,63062
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40770 Å2
ΔGint-344 kcal/mol
Surface area95360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.680, 177.395, 229.445
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
M17 LEUCYL-AMINOPEPTIDASE


Mass: 57564.648 Da / Num. of mol.: 12 / Mutation: N68Q, N431Q, N462Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate HB3) (eukaryote)
Strain: isolate HB3 / Gene: PFHG_04072 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0L7KHE6

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Non-polymers , 9 types, 2310 molecules

#2: Chemical
ChemComp-J4V / (1R,2r,3S,5R,7R)-N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]tricyclo[3.3.1.1~3,7~]decane-2-carboxamide


Mass: 458.473 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C25H25F3N2O3
#3: Chemical
ChemComp-CO3 / CARBONATE ION


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


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2199 / 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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 30% PEG400, 0.2M Li2SO4, 0.1M Tris pH 8

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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, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→48.88 Å / Num. obs: 311885 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 27.8 Å2 / Rmerge(I) obs: 0.253 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.512 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.9data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.17 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 15467 4.97 %
Rwork0.193 --
obs0.196 311114 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46814 0 960 2199 49973
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00848715
X-RAY DIFFRACTIONf_angle_d1.09866071
X-RAY DIFFRACTIONf_dihedral_angle_d13.78817630
X-RAY DIFFRACTIONf_chiral_restr0.1377594
X-RAY DIFFRACTIONf_plane_restr0.0058305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.36354720.27249714X-RAY DIFFRACTION99
2.3261-2.35350.33135300.25999774X-RAY DIFFRACTION100
2.3535-2.38220.31714880.25239884X-RAY DIFFRACTION100
2.3822-2.41240.32795210.24829816X-RAY DIFFRACTION100
2.4124-2.44410.31385340.2449752X-RAY DIFFRACTION100
2.4441-2.47760.31355340.24219773X-RAY DIFFRACTION100
2.4776-2.5130.32325430.24149774X-RAY DIFFRACTION100
2.513-2.55050.30195560.23169766X-RAY DIFFRACTION100
2.5505-2.59030.30935330.23489817X-RAY DIFFRACTION100
2.5903-2.63280.29965100.23319830X-RAY DIFFRACTION100
2.6328-2.67820.30655120.2379786X-RAY DIFFRACTION100
2.6782-2.72690.29485310.22879832X-RAY DIFFRACTION100
2.7269-2.77930.30395160.22569758X-RAY DIFFRACTION100
2.7793-2.83610.30665110.22349828X-RAY DIFFRACTION100
2.8361-2.89770.29994630.22499899X-RAY DIFFRACTION100
2.8977-2.96510.25544820.2089822X-RAY DIFFRACTION100
2.9651-3.03930.26054940.21279827X-RAY DIFFRACTION100
3.0393-3.12140.27285090.21439834X-RAY DIFFRACTION100
3.1214-3.21320.27235330.21819829X-RAY DIFFRACTION100
3.2132-3.31690.27135480.20559791X-RAY DIFFRACTION100
3.3169-3.43550.24015130.19089865X-RAY DIFFRACTION100
3.4355-3.5730.23134690.17859880X-RAY DIFFRACTION100
3.573-3.73550.22254970.17139905X-RAY DIFFRACTION100
3.7355-3.93240.20694630.15949990X-RAY DIFFRACTION100
3.9324-4.17860.19225070.15659930X-RAY DIFFRACTION100
4.1786-4.5010.17965430.14339930X-RAY DIFFRACTION100
4.501-4.95360.18594970.139610004X-RAY DIFFRACTION100
4.9536-5.66940.20775710.16139939X-RAY DIFFRACTION100
5.6694-7.13910.22255190.174610124X-RAY DIFFRACTION100
7.1391-48.17710.17945680.16869974X-RAY DIFFRACTION96

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