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- PDB-5xm7: Crystal structure of Plasmodium falciparum aminopeptidase N in co... -

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Basic information

Entry
Database: PDB / ID: 5xm7
TitleCrystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-((2S,3R)-3-amino-2-hydroxy-4-phenylbutanamido)-N-hydroxy-4-methylpentanamide
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Aminopeptidase / M1-class / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / nucleus ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / nucleus / membrane / cytoplasm
Similarity search - Function
Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold ...Aminopeptidase N, middle-beta domain / Peptidase M1, alanyl aminopeptidase, C-terminal domain / Peptidase M1, alanyl aminopeptidase / Peptidase M1, alanyl aminopeptidase, C-terminal / Peptidase M1, alanyl aminopeptidase, Ig-like fold / Peptidase M1, alanyl aminopeptidase, C-terminal domain superfamily / Alanyl aminopeptidase, Ig-like domain superfamily / Domain of unknown function (DUF3458) Ig-like fold / Domain of unknown function (DUF3458_C) ARM repeats / Zincin-like fold / Zincin-like - #30 / Zincin-like / tricorn interacting facor f3 domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-89X / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsMarapaka, A.K. / Zhang, Y. / Addlagatta, A.
CitationJournal: Chin.Chem.Lett. / Year: 2022
Title: Development of peptidomimetic hydroxamates as PfA-M1 and PfA-M17 dual inhibitors: Biological evaluation and structural characterization by cocrystallization
Authors: Marapaka, A.K. / Sankoju, P. / Zhang, G. / Ding, Y. / Ma, C. / Pillalamarri, V. / Sudhakar, P. / Reddi, B. / Sijwali, P.S. / Zhang, Y. / Addlagatta, A.
History
DepositionMay 12, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_symmetry
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M1 family aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,85517
Polymers106,2911
Non-polymers1,56416
Water6,846380
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-23 kcal/mol
Surface area34690 Å2
Unit cell
Length a, b, c (Å)74.462, 109.103, 112.372
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, 1 molecules A

#1: Protein M1 family aminopeptidase / Pfa-M1


Mass: 106291.477 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 195-1085
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli)
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 396 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-89X / (2S)-4-methyl-N-[(1R)-2-(oxidanylamino)-2-oxidanylidene-1-phenyl-ethyl]-2-[(phenylmethyl)carbamoylamino]pentanamide


Mass: 412.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H28N4O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, or trisaminomethane pH8.5, 0.2M magnesium chloride, 24%PEG2000
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU AFC-5R / Detector: CCD / Date: May 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.96→25 Å / Num. obs: 66352 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.082 / Χ2: 1.058 / Net I/σ(I): 19.8 / Num. measured all: 424528
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.96-2.036.10.34865331.0781100
2.03-2.1160.27665471.0881100
2.11-2.2160.22465741.091100
2.21-2.3260.18265811.0731100
2.32-2.476.10.15265321.0651100
2.47-2.666.20.12266461.0861100
2.66-2.936.50.09366191.041100
2.93-3.356.90.06766401.0261100
3.35-4.227.10.05567211.038199.9
4.22-2570.07869591.02199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.378
Highest resolutionLowest resolution
Rotation24.98 Å2.17 Å

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZO2.3.1data collection
SCALEPACK2.2.0data scaling
MOLREP11.4.05; 02.04.2016model building
PDB_EXTRACT3.22data extraction
DENZO2.3.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X2U

4x2u


Resolution: 1.96→24.976 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2422 / WRfactor Rwork: 0.1852 / FOM work R set: 0.8485 / SU B: 3.554 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1679 / SU Rfree: 0.1546 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2191 3360 5.1 %RANDOM
Rwork0.1684 ---
obs0.171 62705 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.53 Å2 / Biso mean: 31.71 Å2 / Biso min: 5.85 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.96→24.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 100 380 7788
Biso mean--47.34 32.49 -
Num. residues----890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197603
X-RAY DIFFRACTIONr_bond_other_d0.0020.027210
X-RAY DIFFRACTIONr_angle_refined_deg1.831.97310272
X-RAY DIFFRACTIONr_angle_other_deg1.3553.00316653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6465905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48525.027374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.88151380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4911529
X-RAY DIFFRACTIONr_chiral_restr0.1190.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028490
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021752
LS refinement shellResolution: 1.96→2.011 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 239 -
Rwork0.184 4523 -
all-4762 -
obs--98.06 %

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