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- PDB-5cbm: Crystal structure of PfA-M17 with virtual ligand inhibitor -

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Basic information

Entry
Database: PDB / ID: 5cbm
TitleCrystal structure of PfA-M17 with virtual ligand inhibitor
ComponentsM17 family aminopeptidase
KeywordsHYDROLASE / M17 LEUCYL-AMINOPEPTIDASE / PROTEASE / INHIBITOR / HYDROXAMIC ACID
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-4ZN / CARBONATE ION / leucyl aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum Vietnam Oak-Knoll (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRuggeri, C. / Drinkwater, N. / McGowan, S.
CitationJournal: Plos One / Year: 2015
Title: Identification and Validation of a Potent Dual Inhibitor of the P. falciparum M1 and M17 Aminopeptidases Using Virtual Screening.
Authors: Ruggeri, C. / Drinkwater, N. / Sivaraman, K.K. / Bamert, R.S. / McGowan, S. / Paiardini, A.
History
DepositionJul 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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: M17 family aminopeptidase
B: M17 family aminopeptidase
C: M17 family aminopeptidase
D: M17 family aminopeptidase
E: M17 family aminopeptidase
F: M17 family aminopeptidase
G: M17 family aminopeptidase
H: M17 family aminopeptidase
I: M17 family aminopeptidase
J: M17 family aminopeptidase
K: M17 family aminopeptidase
L: M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)705,396114
Polymers690,77612
Non-polymers14,620102
Water58,0263221
1
A: M17 family aminopeptidase
B: M17 family aminopeptidase
C: M17 family aminopeptidase
D: M17 family aminopeptidase
E: M17 family aminopeptidase
F: M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,67559
Polymers345,3886
Non-polymers7,28753
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36610 Å2
ΔGint-517 kcal/mol
Surface area96480 Å2
MethodPISA
2
G: M17 family aminopeptidase
H: M17 family aminopeptidase
I: M17 family aminopeptidase
J: M17 family aminopeptidase
K: M17 family aminopeptidase
L: M17 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)352,72155
Polymers345,3886
Non-polymers7,33349
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35940 Å2
ΔGint-410 kcal/mol
Surface area96880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.092, 177.728, 230.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 family aminopeptidase


Mass: 57564.648 Da / Num. of mol.: 12 / Fragment: UNP residues 87-605 / Mutation: N152Q,N515Q,N563Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum Vietnam Oak-Knoll (FVO) (eukaryote)
Gene: PFFVO_05086 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A024V0B1

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Non-polymers , 7 types, 3323 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-4ZN / (2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid


Mass: 299.303 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H22NO4P
#5: Chemical...
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3221 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
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: Apr 23, 2015
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: 2.3→48.98 Å / Num. obs: 315610 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 24.19 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.482 / Rpim(I) all: 0.182 / Net I/σ(I): 4.9 / Num. measured all: 2509800 / Scaling rejects: 1303
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3483.6361.1122968154620.4461.37199.7
12.6-48.987.30.06611.51526621050.9940.02698.4

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.3.8data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 2.3→48.976 Å / FOM work R set: 0.7737 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2346 15682 4.98 %
Rwork0.1821 299248 -
obs0.1848 314930 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.33 Å2 / Biso mean: 26.91 Å2 / Biso min: 8.32 Å2
Refinement stepCycle: final / Resolution: 2.3→48.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms46958 0 666 3221 50845
Biso mean--34.3 30.67 -
Num. residues----6173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00848466
X-RAY DIFFRACTIONf_angle_d1.08865701
X-RAY DIFFRACTIONf_chiral_restr0.0417554
X-RAY DIFFRACTIONf_plane_restr0.0058291
X-RAY DIFFRACTIONf_dihedral_angle_d14.60417254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32620.37575100.312798751038599
2.3262-2.35350.3595160.2868986910385100
2.3535-2.38220.35065100.2925991210422100
2.3822-2.41240.33654950.2717993610431100
2.4124-2.44410.33325480.2664981210360100
2.4441-2.47760.29115410.2517988210423100
2.4776-2.5130.31375570.2518990110458100
2.513-2.55050.28515470.239982910376100
2.5505-2.59040.31435600.2437989410454100
2.5904-2.63280.29235050.2287993910444100
2.6328-2.67820.30675240.2289994310467100
2.6782-2.72690.26715200.2216987010390100
2.7269-2.77940.27635470.2061993210479100
2.7794-2.83610.27365150.2005991310428100
2.8361-2.89780.28044750.20061001910494100
2.8978-2.96520.25394940.1971000410498100
2.9652-3.03930.26514910.1923996010451100
3.0393-3.12150.25815230.1882997510498100
3.1215-3.21330.24095310.181996210493100
3.2133-3.3170.2345580.1719996510523100
3.317-3.43550.21265120.16531000310515100
3.4355-3.5730.19974850.15471002910514100
3.573-3.73560.18994990.13991003610535100
3.7356-3.93250.19154720.13651007810550100
3.9325-4.17870.16595150.1321005010565100
4.1787-4.50120.17345420.12491006510607100
4.5012-4.95370.17234970.11851011210609100
4.9537-5.66960.18685830.14671008610669100
5.6696-7.13960.20525300.15941019810728100
7.1396-48.9870.17335800.1584101991077997

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