8g6e

Structure of the Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304

Method: ELECTRON MICROSCOPY D_max: 196.5 Å Quality: GOOD

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

下载 Download SAXS (.dat) P(r) (.pr.out) CIF

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	8g6e
沉积日期 deposition_date	2023-02-15
结构标题 title	Structure of the Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304
关键词 keywords	proteasome, inhibitor, 20S, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
实验方法 method	ELECTRON MICROSCOPY

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	60.25 Å
回转半径 Rg (电子) rg_electron	59.76 Å
零角强度 I(0) i0	7400530000.00
分子量 molecular_weight	739420.0 kDa
排除体积 excluded_volume	929780 Å³
包络体积 envelope_volume	1292800 Å³
水化壳体积 shell_volume	172050 Å³
包络直径 envelope_diameter	197.3 Å
壳层 Rg shell_rg	68.54 Å
包络 Rg envelope_rg	58.00 Å
形状 Rg shape_rg	59.73 Å
总 Rg total_rg	60.03 Å
总原子数 total_atoms	52006
残基数 n_residues	6490
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	196.5 Å
Rg (实空间) rg_real	59.94 Å
Rg 误差 (实空间) rg_real_error	1.60 Å
I(0) (实空间) i0_real	7.4000e+09
I(0) 误差 (实空间) i0_real_error	1.6970e+08
Rg (倒空间) rg_reciprocal	60.48 Å
I(0) (倒空间) i0_reciprocal	7407000000.0000
解质量估计 total_estimate	0.8597
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	75.6 Å
偏度 Skewness skewness	0.196
峰度 Kurtosis kurtosis	-0.417
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	1209000000.0000
实空间数据点数 n_real_points	27
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.835

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (16)

Entity 1 polymer

描述 description	Proteasome subunit alpha type-6
分子量 formula_weight	29531.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,O
原子数 atom_count	52266

MVRPSQSMYDRHLTIFSPDGNLYQIEYAIKAVKNTNITSVGVKGENCAVIISQKKMATQYISQDKLLDYNNITNIYNITDEIGCSMVGMPGDCLSMVYKARSEASEFLYSNGYNVNAETLCRNICDKIQVYTQHAYMRLHACSGMIIGIDENNKPELFKFDPSGFCAGYRACVIGNKEQESISVLERLLEKRKKKIQQETIDEDIRNTTILAIEALQTILAFDLKASEIEVAIVSTKNRNFTQISEKEIDNYLTYIAERD

Entity 2 polymer

描述 description	Proteasome subunit alpha type-2
分子量 formula_weight	26556.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	B,P

MADGEYSFSLTTFSPTGKLVQIEYALNRVSSSSPALGIRAKNGVIIATEKKSPNELIEENSIFKIQQISEHIGIVYAGMPGDFRVLLKRARKEAIRYSLQYGSEILVKELVKIIASIVQEFTQTGGVRPFGLSLLICGVDVYGYHLYQIDPSGCYFNWMATCVGKDYQNNMSFLEKRYNKDIEIEDAIHTAILTLKESYEGVLNEKNIEIGVAYDNKPFKILTQNEIKDYLIEIE

Entity 3 polymer

描述 description	Proteasome subunit alpha type
分子量 formula_weight	27977.7 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	C,Q

MARRYDSRTTTFSPEGRLYQVEYALEAINNASITIGLITKDGVILGADKVFISKLIDKANNYEKIYKIDKHIFCGVAGLNADANILINQSRLYAQRYLYNYNEVQPVSQLVVQICDIKQSYTQYGGLRPYGVSFLIGGYDTKDGYQLYHTDPSGNYSGWFATAIGTNNLTASSVLKQEWKNDMTLEEGLLLALKTLAKSTDTEIPKSEKIELAYLTNKDGEVYQKYLTEKEIEELIKLYTQKYIKE

Entity 4 polymer

描述 description	Proteasome subunit alpha type
分子量 formula_weight	27263.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	D,R

MSYDRAITVFSPDGHLLQVEHALEAVKKGGCAVAIKSSNFAVLAVEKKNIPKLQNPKTTEKLIKLDEHNCLAFAGLNADARVLVNKTRLECQRYYLNMDEPAPVDYIAKYVAKVQQKFTHRGGVRPFGIATLIAGFKNNKEICIYQTEPSGIYAAWKAQAIGKNAKIVQEFLEKNYQENMEQKDCIFLALKAIFEVVELSSKNVEVALLTEKDLTFIEEQEINSMVELIDQERTKNNEQNE

Entity 5 polymer

描述 description	Proteasome subunit alpha type
分子量 formula_weight	28417.4 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	E,S

MFSTRSEYDRGVNTFSPEGRLFQVEYALGAIKLGSTAVGICVNDGVILASERRISSTLIEKDSVEKLLSIDDHIGCAMSGLMADARTLIDYARVECNHYKFIYNENINIKSCVELISELALDFSNLSDSKRKKIMSRPFGVALLIGGVDKNGPCLWYTEPSGTNTRFSAASIGSAQEGAELLLQENYKKDMTFEQAEILALTVLRQVMEDKLSTSNVEICAIKKSDQTFYKYNTDDISRIIDVLPSPVYPTIDMTA

Entity 6 polymer

描述 description	Proteasome subunit alpha type-1
分子量 formula_weight	28742.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	F,T

MYRNLYDTDNIIYSPEGRLYQVEYASEAIKQGTCAVAIKSKDYVVVSGLKKCISKLSFPQEKIFKIDDYIGISMSGITSDAKVLTKFMQNECLSHKFLYNENINIESLVRSVADKYQKNTQKSSKRAFGVGLMIAAYHNEPCIFETRPNGSYFEYDALSFGARSHASKTYLEKNLHLFEECSLEELILHCLKALKCSLSSESELTISNTALAVVGKNHPWQEISSLQLEEYLSKVKMDAEQEQVEENVQNEAN

Entity 7 polymer

描述 description	Proteasome subunit alpha type-3
分子量 formula_weight	29324.3 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	G,U

MAGLSAGYDLSVSTFSPDGRLYQVEYIYKSINNNNTALCLECKDGIICCCINSNMDKNKMIKKNSYNRIYHVNNNIIITYSGFDGDARNIIDRARSEANTYYYNFHTNIPLHILVNRISLYIHAYTLYWHMRPFAASIIISSFNEKDKGDIYCIEPNGACYKYSGIVIGKNKEMFKTEIEKKDYKDINVRDAIEDIYKFILTSDDHMNKNNLQNLVNFSWICKESSYEFQNIHEEILTPALNKAVEYIEKLN

Entity 8 polymer

描述 description	Proteasome subunit beta type-6
分子量 formula_weight	29143.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	H,V

TTIIGIIYDNGVMLACDSRTSSGTFISNKCSRKINRINENLYVCRSGASAHSQKIIEIIKHYCVSMKNENRKKGRFHEGETIYDETTYDEEIDIDSINYLDYNNNNDNNLVTKNKYFYEDKFNDYNPLVENVAHITKKIIYTNNNFLSCALIFGGYDKIKKQQLYAVNLNGSIIEKHDFAVSGSGSIYIQSYLQDKYKKFMTKKECFNLILNCVKYAMHNDNSSGGLIRIVNITKSFVEEFTVVNTQMNFQY

Entity 9 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	25104.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	I,W

TTICGLVCQNAVILGADTRATEGPIVADKNCSKLHYISKNIWCAGAGVAGDLEHTTLWLQHNVELHRLNTNTQPRVSMCVSRLTQELFKYQGYKVCAIVLGGVDVNGPQLYGIHPHGSSCLLPFTALGSGSLNAMAVLEAKYRDNMTIEEGKNLVCEAICAGIFNDLGSGGNVDICVITKDSYQHIRPYKEPNMRLYHLPHPTIYPKGTTPILSEKIEYIKKFISVEDA

Entity 10 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	24533.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	J,X

MGSIYNYNGGCVLGMSGSNCVAIACDLRLGANTFTTVSTKFSKIFKMNNNVYVGLSGLATDIQTLYEILRYRVNLYEVRQDAEMDVECFANMLSSILYSNRFSPYFVNPIVVGFKLKHYVDEEGEKKVNYEPYLTAYDLIGAKCETRDFVVNGVTSEQLFGMCESLYVKDQDENGLFETISQCLLSALDRDCISGWGAEVLVLTPEKIIKKKLKARMD

Entity 11 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	22889.1 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	K,Y

MDTLIGLRGNNFVVLAADTYSINSIIKLKNDDNTKFYDIHGNKCLLLGGSIGDRLQFGEFIRKNVHLYQYQNNTDMFVKSFAFFTRKNLAYYLRRNPFEVNCLIAGYDKKDGYQLYWCDYLSNMDSVNKGAHGYGAYLVSAILDKYYHENLTVDEALDIFKLCFEELKKRFLLTQINYELRIMYDNKVETQYVTV

Entity 12 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	23620.6 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	L,Z

TTTLAFKFKDGIIVAVDSRASMGSFISSQNVEKIIEINKNILGTMAGGAADCLYWEKYLGKIIKIYELRNNEKISVRAASTILSNILYQYKGYGLCCGIILSGYDHTGFNMFYVDDSGKKVEGNLFSCGSGSTYAYSILDSAYDYNLNLDQAVELARNAIYHATFRDGGSGGKVRVFHIHKNGYDKIIEGEDVFDLHYHYTNPEQKDQYVM

Entity 13 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	27301.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	M,a

MDLILYNDNLTEKKTEKENVIEHGRGFKRWYPYIDNGGTVIGLTGKDYVILAADTRLSLSYSIYTRFCPKISKLTDKCIIGSSGMQSDIKTLHSLLQKKIQLFVLEHSHYPDIHVIARLLCVILYSRRFFPYYAFNILAGVDENNKGVLYNYDSVGSYCEATHSCVGSGSQLILPILDNRVEQKNQLIKNTNFNLGDDINFVKDAITSATERDIYTGDKTLIYVIDKMGINVNTLDLKQD

Entity 14 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	30909.9 kDa
来源方法 src_method	nat
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	N,b

MTLGPVVTGTSVIAIKYKHGIMIAADRKASYGSYAKFQNVERIFKINNKTVMGFSGELADAQYLHELLTRKNINNLSEKKRKEDMYTPQHYHSYVSRVFYVRKNRIDPLFNNIIIAGINSQKYDNNDDNVLLYTNKNNDDEQNEYKNNEEYKEIHKDDLYIGFVDMHGTNFCDDYITTGYARYFALTLLRDHYKDNMTEEEARILINECLRILYFRDATSSNFIQIVKVTSKGVEYEEPYILPCVLNSADYVYPSTLLPPAGCMW

Entity 15 non-polymer

描述 description	;(7S,10S,13S)-N-cyclopentyl-10-[2-(morpholin-4-yl)ethyl]-9,12-dioxo-13-(2-oxopyrrolidin-1-yl)-2-oxa-8,11-diazabicyclo[13.3.1]nonadeca-1(19),15,17-triene-7-carboxamide ;
分子量 formula_weight	597.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	6

Entity 16 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	218

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7. 引用文献 (1)

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晶胞边长 a length_a	1.000 Å
晶胞边长 b length_b	1.000 Å
晶胞边长 c length_c	1.000 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	—

空间群 space_group	P 1
空间群编号 int_tables_number	1
晶系 crystal_system	—

分辨率 resolution	2.18 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	305581

fit	/app/data/saxs_computation/g6/8g6e/8g6e.fit
pddf	/app/data/pr_computation/g6/8g6e/8g6e.pr.out
profile	/app/data/saxs_computation/g6/8g6e/8g6e.dat

Structure of the Plasmodium falciparum 20S proteasome complexed with inhibitor TDI-8304

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

冷冻电镜 EM 3D

5. 实体与聚合体信息 (16)

Entity 1 polymer

聚合体 Polymer

Entity 2 polymer

聚合体 Polymer

Entity 3 polymer

聚合体 Polymer

Entity 4 polymer

聚合体 Polymer

Entity 5 polymer

聚合体 Polymer

Entity 6 polymer

聚合体 Polymer

Entity 7 polymer

聚合体 Polymer

Entity 8 polymer

聚合体 Polymer

Entity 9 polymer

聚合体 Polymer

Entity 10 polymer

聚合体 Polymer

Entity 11 polymer

聚合体 Polymer

Entity 12 polymer

聚合体 Polymer

Entity 13 polymer

聚合体 Polymer

Entity 14 polymer

聚合体 Polymer

Entity 15 non-polymer

Entity 16 water

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)