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- PDB-7rie: Plasmodium falciparum M17 in complex with inhibitor MIPS2571 -

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Basic information

Entry
Database: PDB / ID: 7rie
TitlePlasmodium falciparum M17 in complex with inhibitor MIPS2571
ComponentsM17 leucyl aminopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Aminopeptidase / Enzyme / Malaria / PEPTIDE BINDING PROTEIN / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding ...Hydrolases; Acting on peptide bonds (peptidases); Dipeptidases / leucyl aminopeptidase / metallodipeptidase activity / peptide catabolic process / metalloaminopeptidase activity / carboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / zinc ion binding / identical protein binding / metal ion binding / cytoplasm / cytosol
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 / Macro domain-like
Similarity search - Domain/homology
Chem-5IF / CARBONATE ION / Leucine aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWebb, C.T. / McGowan, S.
Funding support1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)
CitationJournal: Elife / Year: 2022
Title: Genetic and chemical validation of Plasmodium falciparum aminopeptidase Pf A-M17 as a drug target in the hemoglobin digestion pathway.
Authors: Edgar, R.C.S. / Siddiqui, G. / Hjerrild, K. / Malcolm, T.R. / Vinh, N.B. / Webb, C.T. / Holmes, C. / MacRaild, C.A. / Chernih, H.C. / Suen, W.W. / Counihan, N.A. / Creek, D.J. / Scammells, P. ...Authors: Edgar, R.C.S. / Siddiqui, G. / Hjerrild, K. / Malcolm, T.R. / Vinh, N.B. / Webb, C.T. / Holmes, C. / MacRaild, C.A. / Chernih, H.C. / Suen, W.W. / Counihan, N.A. / Creek, D.J. / Scammells, P.J. / McGowan, S. / de Koning-Ward, T.F.
History
DepositionJul 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 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

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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)712,70180
Polymers702,93312
Non-polymers9,76868
Water27,5091527
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)356,42240
Polymers351,4676
Non-polymers4,95534
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)356,28040
Polymers351,4676
Non-polymers4,81334
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)175.290, 175.858, 234.679
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 86 or (resid 87 and (name...
d_2ens_1(chain "B" and (resid 86 through 101 or (resid 102...
d_3ens_1(chain "C" and (resid 86 or (resid 87 and (name...
d_4ens_1(chain "D" and (resid 86 through 101 or (resid 102...
d_5ens_1(chain "E" and (resid 86 through 112 or (resid 113...
d_6ens_1(chain "F" and (resid 86 through 101 or (resid 102...
d_7ens_1(chain "G" and (resid 86 or (resid 87 and (name...
d_8ens_1(chain "H" and (resid 86 through 101 or (resid 102...
d_9ens_1(chain "I" and (resid 86 through 101 or (resid 102...
d_10ens_1(chain "J" and (resid 86 through 101 or (resid 102...
d_11ens_1(chain "K" and (resid 86 or (resid 87 and (name...
d_12ens_1(chain "L" and (resid 86 through 101 or (resid 102...

NCS oper:
IDCodeMatrixVector
1given(-0.498876653656, -0.390559932989, 0.773682766501), (0.370423700683, 0.710968935586, 0.597753673852), (-0.783523047784, 0.584795786044, -0.210013147722)71.9810192057, -70.9780154637, 146.739253794
2given(-0.502624861646, 0.372006164427, -0.780371489794), (-0.377682972852, 0.717489698633, 0.585289761035), (0.777639904116, 0.588914209357, -0.220127766408)177.063673044, -8.73873836344, 18.9594883135
3given(0.520434241624, 0.408925133623, -0.749618859979), (0.392989456664, -0.894080961867, -0.214891881136), (-0.758094642572, -0.182755215298, -0.626013613418)86.9187076259, 92.1700629028, 226.63813243
4given(0.478089998943, -0.389488722787, 0.787228358059), (-0.359199306099, -0.90462136751, -0.229425456178), (0.801502221711, -0.173085863855, -0.572394507595)-9.87567303324, 156.723164044, 91.2560939635
5given(-0.999580529989, 0.00356685130029, -0.0287409401076), (0.0209720717697, -0.595258090474, -0.803260840531), (-0.0199733891004, -0.803526653756, 0.594933593295)167.933097254, 161.970254312, 84.775615643
6given(0.999911534062, 0.00452211292489, 0.0125089785361), (-0.00449218169745, 0.999986982247, -0.00241984304873), (-0.0125197585008, 0.00236343637061, 0.999918831614)3.98881896259, 0.599165710811, -115.816288809
7given(-0.505963534059, -0.382648614339, 0.773033595742), (0.376557922411, 0.708311729518, 0.59707505801), (-0.776018706779, 0.593190131216, -0.214290538653)77.6196743724, -71.2476301961, 29.2373277695
8given(-0.49616165521, 0.382974769492, -0.779200832797), (-0.376301484766, 0.713931310948, 0.590507642466), (0.782445400308, 0.586201679612, -0.210111366558)181.169454376, -9.14976963383, -98.9622175158
9given(0.513018726882, 0.404072693069, -0.75732228581), (0.392620364989, -0.895031838742, -0.211582741813), (-0.76332236628, -0.188794243434, -0.617815262666)93.9556433746, 91.9024531532, 109.857098396
10given(0.482449250631, -0.393803569712, 0.782407482741), (-0.361563026389, -0.90312081872, -0.231613826751), (0.797818838155, -0.171147700177, -0.578094772688)-4.11563416474, 156.996771474, -24.7932379027
11given(-0.999619800641, -0.00671274420406, -0.0267430968956), (0.0254982896206, -0.594141934411, -0.803955968322), (-0.010492444555, -0.804332208009, 0.594087205524)173.729062344, 161.599710161, -32.6200470545

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
M17 leucyl aminopeptidase


Mass: 58577.777 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IL11, leucyl aminopeptidase

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Non-polymers , 6 types, 1595 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical
ChemComp-5IF / N-{(1R)-2-(hydroxyamino)-1-[4'-(hydroxymethyl)[1,1'-biphenyl]-4-yl]-2-oxoethyl}-2,2-dimethylpropanamide


Mass: 356.416 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C20H24N2O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1527 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 52.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, 0.2M LiSO4, 0.1M Tris pH 7.5 to 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953727 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953727 Å / Relative weight: 1
ReflectionResolution: 2.49→48.8 Å / Num. obs: 250390 / % possible obs: 99.5 % / Redundancy: 6.9 % / Biso Wilson estimate: 41.46 Å2 / CC1/2: 0.996 / Net I/σ(I): 6.9
Reflection shellResolution: 2.49→2.54 Å / Redundancy: 6.5 % / Num. unique obs: 11256 / CC1/2: 0.683 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KQZ

3kqz


Resolution: 2.49→48.75 Å / SU ML: 0.3238 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.1335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 12429 4.97 %
Rwork0.1953 237673 -
obs0.1969 250102 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.18 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47006 0 528 1527 49061
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003148430
X-RAY DIFFRACTIONf_angle_d0.570665734
X-RAY DIFFRACTIONf_chiral_restr0.04457558
X-RAY DIFFRACTIONf_plane_restr0.00358323
X-RAY DIFFRACTIONf_dihedral_angle_d6.81266692
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.405553780777
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.440643941227
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.894029676062
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.843571002632
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.843657237696
ens_1d_7AX-RAY DIFFRACTIONTorsion NCS0.303639774483
ens_1d_8AX-RAY DIFFRACTIONTorsion NCS0.431892486678
ens_1d_9AX-RAY DIFFRACTIONTorsion NCS0.401156460973
ens_1d_10AX-RAY DIFFRACTIONTorsion NCS0.875634175724
ens_1d_11AX-RAY DIFFRACTIONTorsion NCS0.843648917641
ens_1d_12AX-RAY DIFFRACTIONTorsion NCS0.827082126175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.520.38923840.32226793X-RAY DIFFRACTION86.51
2.52-2.550.31253970.27787959X-RAY DIFFRACTION99.99
2.55-2.580.30884480.26937854X-RAY DIFFRACTION100
2.58-2.620.31334190.26137902X-RAY DIFFRACTION99.95
2.62-2.650.3184240.2577841X-RAY DIFFRACTION99.96
2.65-2.690.29813960.24127909X-RAY DIFFRACTION99.99
2.69-2.720.29313950.2437923X-RAY DIFFRACTION100
2.72-2.760.28864240.24067899X-RAY DIFFRACTION99.99
2.76-2.810.28754320.23547858X-RAY DIFFRACTION100
2.81-2.850.27694230.23517913X-RAY DIFFRACTION100
2.85-2.90.27964630.23087874X-RAY DIFFRACTION99.99
2.9-2.960.27823860.23257960X-RAY DIFFRACTION99.98
2.96-3.010.27233830.23787933X-RAY DIFFRACTION99.99
3.01-3.070.27264080.23047946X-RAY DIFFRACTION99.99
3.07-3.140.2824120.23277940X-RAY DIFFRACTION99.96
3.14-3.210.25793910.21987938X-RAY DIFFRACTION100
3.21-3.290.24944030.21727947X-RAY DIFFRACTION99.99
3.29-3.380.25894360.21147926X-RAY DIFFRACTION99.99
3.38-3.480.24924260.20857906X-RAY DIFFRACTION100
3.48-3.60.25144210.20657973X-RAY DIFFRACTION99.99
3.6-3.720.20584120.18397952X-RAY DIFFRACTION99.98
3.72-3.870.20443980.17467973X-RAY DIFFRACTION99.94
3.87-4.050.21054010.16657992X-RAY DIFFRACTION99.99
4.05-4.260.20963860.15868030X-RAY DIFFRACTION99.95
4.26-4.530.1624580.14297974X-RAY DIFFRACTION100
4.53-4.880.17113790.14578065X-RAY DIFFRACTION99.93
4.88-5.370.18093970.16048029X-RAY DIFFRACTION99.91
5.37-6.150.2124450.18388062X-RAY DIFFRACTION99.95
6.15-7.740.18244390.17688144X-RAY DIFFRACTION99.98
7.74-48.750.15954430.16088258X-RAY DIFFRACTION98.28

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