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- PDB-5y1t: Crystal structure of Plasmodium falciparum aminopeptidase N in co... -

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Basic information

Entry
Database: PDB / ID: 5y1t
TitleCrystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(2,3-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide
ComponentsM1 family aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / M1-class Aminopeptidase / 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-E8G / Aminopeptidase N
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.14 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
DepositionJul 21, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 1, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_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)107,10610
Polymers106,2911
Non-polymers8149
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-27 kcal/mol
Surface area34680 Å2
Unit cell
Length a, b, c (Å)74.450, 109.285, 112.275
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)
Strain: isolate FcB1 / Columbia / Production host: Escherichia coli (E. coli)
References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 370 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-E8G / (2S)-2-[(2,3-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide


Mass: 307.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 44.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris, pH 8.5, 0.2M Magnesium chloride, 24% PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.14→25 Å / Num. obs: 50855 / % possible obs: 98.9 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.026 / Rrim(I) all: 0.053 / Χ2: 1.046 / Net I/σ(I): 25.5 / Num. measured all: 206469
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.14-2.223.60.12750280.9810.0770.151.06499.9
2.22-2.313.70.10350650.9880.0620.1211.054100
2.31-2.413.80.08951140.9910.0530.1041.0499.9
2.41-2.543.90.07350560.9940.0420.0841.02699.9
2.54-2.74.10.06150760.9960.0340.071.04199.7
2.7-2.94.20.05150930.9970.0280.0591.08699.6
2.9-3.24.40.04450910.9980.0240.051.00599.3
3.2-3.664.40.03950870.9970.0210.0451.05598.4
3.66-4.64.30.0450680.9960.0220.0461.01597.3
4.6-254.30.0451770.9970.0210.0451.07395.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.336
Highest resolutionLowest resolution
Rotation24.97 Å2.35 Å

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Processing

Software
NameVersionClassificationNB
DENZO2.3.1data collection
SCALEPACK2.2.0data scaling
MOLREP11.4.05model building
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
DENZO2.3.1data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X2U

4x2u


Resolution: 2.14→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.642 / SU ML: 0.123 / SU R Cruickshank DPI: 0.2394 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.195
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 2521 5 %RANDOM
Rwork0.1644 ---
obs0.1673 48249 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.44 Å2 / Biso mean: 27.828 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.14→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 50 361 7719
Biso mean--51.28 26.36 -
Num. residues----890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197535
X-RAY DIFFRACTIONr_bond_other_d0.0020.027144
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.96910186
X-RAY DIFFRACTIONr_angle_other_deg1.0313.00216496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92725.027372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.489151376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0461529
X-RAY DIFFRACTIONr_chiral_restr0.1080.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021735
LS refinement shellResolution: 2.136→2.191 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 216 -
Rwork0.152 3398 -
all-3614 -
obs--95.86 %

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