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- PDB-4zy1: X-ray crystal structure of PfA-M17 in complex with hydroxamic aci... -

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Basic information

Entry
Database: PDB / ID: 4zy1
TitleX-ray crystal structure of PfA-M17 in complex with hydroxamic acid-based inhibitor 10r
ComponentsProbable M17 family 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
Chem-4U5 / CARBONATE ION / leucyl aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum FcB1/Columbia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDrinkwater, N. / McGowan, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1063786 Australia
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: Potent dual inhibitors of Plasmodium falciparum M1 and M17 aminopeptidases through optimization of S1 pocket interactions.
Authors: Drinkwater, N. / Vinh, N.B. / Mistry, S.N. / Bamert, R.S. / Ruggeri, C. / Holleran, J.P. / Loganathan, S. / Paiardini, A. / Charman, S.A. / Powell, A.K. / Avery, V.M. / McGowan, S. / Scammells, P.J.
History
DepositionMay 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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 / 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)710,158109
Polymers695,78712
Non-polymers14,37197
Water26,0321445
1
A: Probable M17 family aminopeptidase
B: Probable M17 family aminopeptidase
C: Probable M17 family aminopeptidase
D: Probable M17 family aminopeptidase
E: Probable M17 family aminopeptidase
F: Probable M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,60251
Polymers347,8936
Non-polymers6,70945
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27690 Å2
ΔGint-126 kcal/mol
Surface area96270 Å2
MethodPISA
2
G: Probable M17 family aminopeptidase
H: Probable M17 family aminopeptidase
I: Probable M17 family aminopeptidase
J: Probable M17 family aminopeptidase
K: Probable M17 family aminopeptidase
L: Probable M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,55558
Polymers347,8936
Non-polymers7,66252
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27460 Å2
ΔGint-123 kcal/mol
Surface area95820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.097, 177.325, 229.648
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
Probable M17 family aminopeptidase


Mass: 57982.230 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 FcB1/Columbia (eukaryote)
Strain: isolate FcB1 / Columbia / Plasmid: PTRCHIS-2B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A024V0B1, leucyl aminopeptidase

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Non-polymers , 7 types, 1542 molecules

#2: Chemical
ChemComp-4U5 / N-{(1R)-2-(hydroxyamino)-1-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]-2-oxoethyl}-2,2-dimethylpropanamide


Mass: 330.382 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H22N4O3
#3: Chemical...
ChemComp-ZN / ZINC ION


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


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


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#6: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1445 / 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: 2.57 Å3/Da / Density % sol: 52.06 %
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
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 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: 2.5→48.9 Å / Num. obs: 232933 / % possible obs: 95.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.301 / Net I/σ(I): 4.9
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.5 % / Rmerge(I) obs: 1.24 / Mean I/σ(I) obs: 1 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 2.5→48.9 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.257 11491 4.95 %
Rwork0.203 --
obs0.205 232204 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.51 Å2
Refinement stepCycle: LAST / Resolution: 2.5→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46949 0 730 1445 49124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348534
X-RAY DIFFRACTIONf_angle_d0.6365813
X-RAY DIFFRACTIONf_dihedral_angle_d13.33417327
X-RAY DIFFRACTIONf_chiral_restr0.0257540
X-RAY DIFFRACTIONf_plane_restr0.0038325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.52840.42383360.33797425X-RAY DIFFRACTION97
2.5284-2.55820.35974140.3187349X-RAY DIFFRACTION96
2.5582-2.58940.41124030.32627381X-RAY DIFFRACTION96
2.5894-2.62210.3334070.30977415X-RAY DIFFRACTION96
2.6221-2.65660.33333730.29087380X-RAY DIFFRACTION96
2.6566-2.6930.35263940.29527414X-RAY DIFFRACTION96
2.693-2.73150.35333550.29047448X-RAY DIFFRACTION96
2.7315-2.77230.32263570.27897426X-RAY DIFFRACTION96
2.7723-2.81560.32333770.27097426X-RAY DIFFRACTION96
2.8156-2.86170.33823610.26197344X-RAY DIFFRACTION96
2.8617-2.91110.34354210.25527393X-RAY DIFFRACTION96
2.9111-2.9640.30934180.25077322X-RAY DIFFRACTION96
2.964-3.0210.2934080.24577360X-RAY DIFFRACTION96
3.021-3.08270.31264050.2497353X-RAY DIFFRACTION96
3.0827-3.14970.30453520.24897415X-RAY DIFFRACTION95
3.1497-3.22290.27064000.22777380X-RAY DIFFRACTION96
3.2229-3.30350.27623450.21847355X-RAY DIFFRACTION95
3.3035-3.39280.26793950.19957352X-RAY DIFFRACTION95
3.3928-3.49260.26223860.19767362X-RAY DIFFRACTION95
3.4926-3.60530.25133810.18987364X-RAY DIFFRACTION95
3.6053-3.73410.23513910.18137323X-RAY DIFFRACTION95
3.7341-3.88360.22593300.16847417X-RAY DIFFRACTION95
3.8836-4.06020.21113760.15767303X-RAY DIFFRACTION95
4.0602-4.27420.213970.1517319X-RAY DIFFRACTION94
4.2742-4.54180.17653870.13457321X-RAY DIFFRACTION94
4.5418-4.89220.16963830.13737289X-RAY DIFFRACTION94
4.8922-5.38390.21644000.15117259X-RAY DIFFRACTION93
5.3839-6.16170.2213520.16927304X-RAY DIFFRACTION93
6.1617-7.75810.21784030.16567285X-RAY DIFFRACTION92
7.7581-48.90970.1823840.15497229X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 84.6781 Å / Origin y: 233.5397 Å / Origin z: 35.4785 Å
111213212223313233
T0.0394 Å20.0074 Å2-0.0026 Å2-0.0306 Å2-0.0507 Å2--0.079 Å2
L0.0391 °20.0225 °2-0.0259 °2-0.0249 °2-0.0195 °2--0.0483 °2
S-0.0092 Å °0.0109 Å °-0.0293 Å °0.0005 Å °0.0107 Å °0.0145 Å °0.005 Å °0.0023 Å °0.0044 Å °
Refinement TLS groupSelection details: ALL

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