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9yuy

Structure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.

Method: ELECTRON MICROSCOPY D_max: 174.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yuy
deposition_date	2025-10-23
title	Structure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.
keywords	Proteasome, 20S, Inhibitor, Plasmodium, Covalent, HYDROLASE; HYDROLASE
method	ELECTRON MICROSCOPY

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	60.71 Å
rg_electron	60.28 Å
i0	6797370000.00
molecular_weight	713020.0 kDa
excluded_volume	898210 Å³
envelope_volume	1285800 Å³
shell_volume	171070 Å³
envelope_diameter	194.6 Å
shell_rg	68.35 Å
envelope_rg	58.10 Å
shape_rg	60.34 Å
total_rg	60.20 Å
total_atoms	100048
n_residues	6284
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	174.5 Å
rg_real	60.41 Å
rg_real_error	1.18 Å
i0_real	6.7970e+09
i0_real_error	1.3880e+08
rg_reciprocal	60.94 Å
i0_reciprocal	6803000000.0000
total_estimate	0.8347
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	80.5 Å
skewness	0.197
kurtosis	-0.431
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	1038000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.004

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4. Crystallography & Experiment

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5. Entities & Polymer Info (15)

Entity 1 polymer

description	Proteasome subunit alpha type
formula_weight	27977.7 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,Q
atom_count	100048

MARRYDSRTTTFSPEGRLYQVEYALEAINNASITIGLITKDGVILGADKVFISKLIDKANNYEKIYKIDKHIFCGVAGLNADANILINQSRLYAQRYLYNYNEVQPVSQLVVQICDIKQSYTQYGGLRPYGVSFLIGGYDTKDGYQLYHTDPSGNYSGWFATAIGTNNLTASSVLKQEWKNDMTLEEGLLLALKTLAKSTDTEIPKSEKIELAYLTNKDGEVYQKYLTEKEIEELIKLYTQKYIKE

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 2 polymer

description	Proteasome subunit alpha type
formula_weight	27263.3 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,R

MSYDRAITVFSPDGHLLQVEHALEAVKKGGCAVAIKSSNFAVLAVEKKNIPKLQNPKTTEKLIKLDEHNCLAFAGLNADARVLVNKTRLECQRYYLNMDEPAPVDYIAKYVAKVQQKFTHRGGVRPFGIATLIAGFKNNKEICIYQTEPSGIYAAWKAQAIGKNAKIVQEFLEKNYQENMEQKDCIFLALKAIFEVVELSSKNVEVALLTEKDLTFIEEQEINSMVELIDQERTKNNEQNE

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 3 polymer

description	Proteasome subunit alpha type
formula_weight	28417.4 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,S

MFSTRSEYDRGVNTFSPEGRLFQVEYALGAIKLGSTAVGICVNDGVILASERRISSTLIEKDSVEKLLSIDDHIGCAMSGLMADARTLIDYARVECNHYKFIYNENINIKSCVELISELALDFSNLSDSKRKKIMSRPFGVALLIGGVDKNGPCLWYTEPSGTNTRFSAASIGSAQEGAELLLQENYKKDMTFEQAEILALTVLRQVMEDKLSTSNVEICAIKKSDQTFYKYNTDDISRIIDVLPSPVYPTIDMTA

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 4 polymer

description	Proteasome endopeptidase complex
formula_weight	28871.7 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,T

MYRNLYDTDNIIYSPEGRLYQVEYASEAIKQGTCAVAIKSKDYVVVSGLKKCISKLSFPQEKIFKIDDYIGISMSGITSDAKVLTKFMQNECLSHKFLYNENINIESLVRSVADKYQKNTQKSSKRAFGVGLMIAAYHNEPCIFETRPNGSYFEYDALSFGARSHASKTYLEKNLHLFEECSLEELILHCLKALKCSLSSESELTISNTALAVVGKNHPWQEISSLQLEEYLSKVKMDAEQEQVEENVQNEANE

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 5 polymer

description	Proteasome subunit alpha type-3, putative
formula_weight	29324.3 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,U

MAGLSAGYDLSVSTFSPDGRLYQVEYIYKSINNNNTALCLECKDGIICCCINSNMDKNKMIKKNSYNRIYHVNNNIIITYSGFDGDARNIIDRARSEANTYYYNFHTNIPLHILVNRISLYIHAYTLYWHMRPFAASIIISSFNEKDKGDIYCIEPNGACYKYSGIVIGKNKEMFKTEIEKKDYKDINVRDAIEDIYKFILTSDDHMNKNNLQNLVNFSWICKESSYEFQNIHEEILTPALNKAVEYIEKLN

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 6 polymer

description	Proteasome subunit beta
formula_weight	22889.1 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,Y

MDTLIGLRGNNFVVLAADTYSINSIIKLKNDDNTKFYDIHGNKCLLLGGSIGDRLQFGEFIRKNVHLYQYQNNTDMFVKSFAFFTRKNLAYYLRRNPFEVNCLIAGYDKKDGYQLYWCDYLSNMDSVNKGAHGYGAYLVSAILDKYYHENLTVDEALDIFKLCFEELKKRFLLTQINYELRIMYDNKVETQYVTV

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 7 polymer

description	Proteasome subunit beta
formula_weight	30630.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,Z

MVIASDESFMNEIDNLINDVEDERIDNDELEFCVAPVNVPRNFIKYAQTQNKKLFDFHKGTTTLAFKFKDGIIVAVDSRASMGSFISSQNVEKIIEINKNILGTMAGGAADCLYWEKYLGKIIKIYELRNNEKISVRAASTILSNILYQYKGYGLCCGIILSGYDHTGFNMFYVDDSGKKVEGNLFSCGSGSTYAYSILDSAYDYNLNLDQAVELARNAIYHATFRDGGSGGKVRVFHIHKNGYDKIIEGEDVFDLHYHYTNPEQKDQYVM

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 8 polymer

description	Proteasome subunit beta
formula_weight	27301.2 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,a

MDLILYNDNLTEKKTEKENVIEHGRGFKRWYPYIDNGGTVIGLTGKDYVILAADTRLSLSYSIYTRFCPKISKLTDKCIIGSSGMQSDIKTLHSLLQKKIQLFVLEHSHYPDIHVIARLLCVILYSRRFFPYYAFNILAGVDENNKGVLYNYDSVGSYCEATHSCVGSGSQLILPILDNRVEQKNQLIKNTNFNLGDDINFVKDAITSATERDIYTGDKTLIYVIDKMGINVNTLDLKQD

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 9 polymer

description	Proteasome endopeptidase complex
formula_weight	29531.7 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,O

MVRPSQSMYDRHLTIFSPDGNLYQIEYAIKAVKNTNITSVGVKGENCAVIISQKKMATQYISQDKLLDYNNITNIYNITDEIGCSMVGMPGDCLSMVYKARSEASEFLYSNGYNVNAETLCRNICDKIQVYTQHAYMRLHACSGMIIGIDENNKPELFKFDPSGFCAGYRACVIGNKEQESISVLERLLEKRKKKIQQETIDEDIRNTTILAIEALQTILAFDLKASEIEVAIVSTKNRNFTQISEKEIDNYLTYIAERD

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 10 polymer

description	Proteasome endopeptidase complex
formula_weight	26556.4 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,P

MADGEYSFSLTTFSPTGKLVQIEYALNRVSSSSPALGIRAKNGVIIATEKKSPNELIEENSIFKIQQISEHIGIVYAGMPGDFRVLLKRARKEAIRYSLQYGSEILVKELVKIIASIVQEFTQTGGVRPFGLSLLICGVDVYGYHLYQIDPSGCYFNWMATCVGKDYQNNMSFLEKRYNKDIEIEDAIHTAILTLKESYEGVLNEKNIEIGVAYDNKPFKILTQNEIKDYLIEIE

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 11 polymer

description	Proteasome subunit beta type-6, putative
formula_weight	32641.7 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,V

MDVVNESQIKCHEEKSWDDEYDIKTPISDGTTIIGIIYDNGVMLACDSRTSSGTFISNKCSRKINRINENLYVCRSGASAHSQKIIEIIKHYCVSMKNENRKKGRFHEGETIYDETTYDEEIDIDSINYLDYNNNNDNNLVTKNKYFYEDKFNDYNPLVENVAHITKKIIYTNNNFLSCALIFGGYDKIKKQQLYAVNLNGSIIEKHDFAVSGSGSIYIQSYLQDKYKKFMTKKECFNLILNCVKYAMHNDNSSGGLIRIVNITKSFVEEFTVVNTQMNFQY

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 12 polymer

description	Proteasome subunit beta
formula_weight	29999.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,W

MKLEYINILKEENGGYNFDNLKRNEILKEKGVKFPQFRKTGTTICGLVCQNAVILGADTRATEGPIVADKNCSKLHYISKNIWCAGAGVAGDLEHTTLWLQHNVELHRLNTNTQPRVSMCVSRLTQELFKYQGYKVCAIVLGGVDVNGPQLYGIHPHGSSCLLPFTALGSGSLNAMAVLEAKYRDNMTIEEGKNLVCEAICAGIFNDLGSGGNVDICVITKDSYQHIRPYKEPNMRLYHLPHPTIYPKGTTPILSEKIEYIKKFISVEDA

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 13 polymer

description	Proteasome subunit beta
formula_weight	24533.1 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,X

MGSIYNYNGGCVLGMSGSNCVAIACDLRLGANTFTTVSTKFSKIFKMNNNVYVGLSGLATDIQTLYEILRYRVNLYEVRQDAEMDVECFANMLSSILYSNRFSPYFVNPIVVGFKLKHYVDEEGEKKVNYEPYLTAYDLIGAKCETRDFVVNGVTSEQLFGMCESLYVKDQDENGLFETISQCLLSALDRDCISGWGAEVLVLTPEKIIKKKLKARMD

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 14 polymer

description	Proteasome subunit beta
formula_weight	30909.9 kDa
ec_number	3.4.25.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	N,b

MTLGPVVTGTSVIAIKYKHGIMIAADRKASYGSYAKFQNVERIFKINNKTVMGFSGELADAQYLHELLTRKNINNLSEKKRKEDMYTPQHYHSYVSRVFYVRKNRIDPLFNNIIIAGINSQKYDNNDDNVLLYTNKNNDDEQNEYKNNEEYKEIHKDDLYIGFVDMHGTNFCDDYITTGYARYFALTLLRDHYKDNMTEEEARILINECLRILYFRDATSSNFIQIVKVTSKGVEYEEPYILPCVLNSADYVYPSTLLPPAGCMW

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Spodoptera frugiperda

Entity 15 non-polymer

description	;methyl N-{[(2R)-1-({(5R,8R)-5-[(3-fluorophenyl)methyl]-2,7-dioxo-1,6-diazacyclododecan-8-yl}amino)-1-oxo-3-phenylpropan-2-yl]carbamoyl}-L-valinate ;
formula_weight	625.7 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.700 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.70 Å
resolution_method	—
num_particles	36364

fit	/app/data/saxs_computation/yu/9yuy/9yuy.fit
pddf	/app/data/pr_computation/yu/9yuy/9yuy.pr.out
profile	/app/data/saxs_computation/yu/9yuy/9yuy.dat

Structure of the Plasmodium falciparum 20S proteasome in complex with a beta5-selective covalent syringolin analogue inhibitor.

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (15)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

Entity 9 polymer

Polymer

Source

Entity 10 polymer

Polymer

Source

Entity 11 polymer

Polymer

Source

Entity 12 polymer

Polymer

Source

Entity 13 polymer

Polymer

Source

Entity 14 polymer

Polymer

Source

Entity 15 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)