8olu

;Leishmania tarentolae proteasome 20S subunit in complex with 1-Benzyl-N-(3-(cyclopropylcarbamoyl)phenyl)-6-oxo-1,6-dihydropyridazine-3-carboxamide ;

Method: ELECTRON MICROSCOPY D_max: 192.6 Å Quality: REASONABLE

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	8olu
沉积日期 deposition_date	2023-03-30
结构标题 title	;Leishmania tarentolae proteasome 20S subunit in complex with 1-Benzyl-N-(3-(cyclopropylcarbamoyl)phenyl)-6-oxo-1,6-dihydropyridazine-3-carboxamide ;
关键词 keywords	Proteasome 20S subunit, UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	59.26 Å
回转半径 Rg (电子) rg_electron	58.89 Å
零角强度 I(0) i0	7015480000.00
分子量 molecular_weight	697260.0 kDa
排除体积 excluded_volume	868230 Å³
包络体积 envelope_volume	1215200 Å³
水化壳体积 shell_volume	165120 Å³
包络直径 envelope_diameter	195.5 Å
壳层 Rg shell_rg	67.17 Å
包络 Rg envelope_rg	57.00 Å
形状 Rg shape_rg	58.88 Å
总 Rg total_rg	59.06 Å
总原子数 total_atoms	48930
残基数 n_residues	6316
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	192.6 Å
Rg (实空间) rg_real	60.16 Å
Rg 误差 (实空间) rg_real_error	0.71 Å
I(0) (实空间) i0_real	6.9020e+09
I(0) 误差 (实空间) i0_real_error	1.2590e+08
Rg (倒空间) rg_reciprocal	59.47 Å
I(0) (倒空间) i0_reciprocal	7021000000.0000
解质量估计 total_estimate	0.6913
解质量评级 solution_quality	REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	74.1 Å
偏度 Skewness skewness	0.324
峰度 Kurtosis kurtosis	-0.168
角度范围 angular_range	— – 0.1300 Å⁻¹
当前正则化参数 α current_alpha	1.4750
最高正则化参数 α highest_alpha	742000000.0000
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: 0.814; Stabil: 0.927; Sysdev: 0.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.810

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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 (15)

Entity 1 polymer

描述 description	Proteasome subunit alpha type
分子量 formula_weight	27178.1 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	A,O
原子数 atom_count	48930

MNRAGFDKYITVFSPEGSLYQVEYAFKAVTYPGLLTVAIRCKDAVLVVTQHLIPDRLMRPDSVTALYEVTPNIGCCMTGRAPDGRALVQRAREEASDYQYRYGVEIPIAVLAKRMGDKAQVRTQQAGLRPMGVVSTFIGMDQSDQDGSLKPQIYTVDPAGWTGGHIACAAGKKQVEAMAFLEKRQKSTELDALTQKEAAMIALAALQSAIGTAVKAKEVEVGRCTAANPAFQRVPNSEVEEWLTAVAEAD

Entity 2 polymer

描述 description	Proteasome subunit alpha type
分子量 formula_weight	25179.6 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	B,P

MSEAFYGLTTFSPSGKLIQIEYATTAAGKGTTALGVKATDGVVIAAKKKAPSTLVDASSIQKVFVLDEHVGCTYSGMGPDCRVLIDSARKNCQQYKLMYNEPIPISQLVRKISAIYQEFTQSGGVRPFGCSLLVAGVDANGYHLYQVDPSGTFWAWKATAIGTGSPDAKAFLEKRYTVDMELEDAVHTALLTLKEGFDGQMTSENTQVGRVVENRFEILSVDQLRDYLDQI

Entity 3 polymer

描述 description	Proteasome subunit alpha type
分子量 formula_weight	32321.4 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	C,Q

MSHRYDSRTTTFSPEGRLYQVEYAVEAIQQAGTVIGVCTKDGVVLAGEKMVPHPLFDSESMQDKNTSGEKMYKIAEHIGCSVAGVTSDAYALLNYARLSALRHQYTFQEPMAIEDLCRILCDEKQLYTQYGGVRPYGVSFLLVGWDRYYGYQLYSTEPSGDYSAWSAYAIGQNDQVAHALLKKDWHESMTLEDGMLLALRVLGKTMDTAKIDLDRVEVAVMRKVPASNIDQLLDPFKHHPKTTPRFQILTRSELKPHAERADQAREAEEKAEAERQRQQEQALES

Entity 4 polymer

描述 description	Proteasome subunit alpha type
分子量 formula_weight	27821.6 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	D,R

MSYDRAITVFSPDGHLFQVEYAQEAVKKGLAAVGVLGSDSVVIAVEKKSAVKLQDSRTIRKIYKVDANIYLAFAGLSADARVLINKAQLECQRFSLNYEDTMDVDMLVRYVAGVQQKSTQSGGSRPFGVATVIGGFNEDGKPHLWKTDPSGMCSAWRAVAIGRHDQTVIEYMEKSYKDGMSRDECVHFAIKSLLEVVESGSRNIELLVLQYKEARYLTEEELQKFVVEVEKEREEEAAAKKKRQAEQE

Entity 5 polymer

描述 description	Proteasome alpha 5 subunit, putative
分子量 formula_weight	38312.3 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	E,S

MLLPRLFSFPVCWSRALSLVCVYHVSLSFPSNSRRLCATPLLPLPCLCKLPAGHSPRKRCLFSFLSCFLDLTYFCIISFLHSVSCHLCFPLRRTRARHPIMFTSKSEYDRGVNTFSPEGRIFQIEYAVEAIKLGSTSLGIRTPEGVVLAAEKRVPSTLVVPSSMSKIMEVDSHIAAVMSGMVADARILVEHARVESQNHRFTYNEPMSVESCTLATCDLSIQFGESGGRRKLMSRPFGVSLLIAGVDEKGPQLWQTDPSGTHTRYDAQAIGGGAEAAQSVFTERYHRNMTLEEGETLAVDILKQVMEDQLSPENIEVAVVRADDGKLHMYTPTEIKAIMSRMPE

Entity 6 polymer

描述 description	Proteasome alpha 1 subunit, putative
分子量 formula_weight	47978.6 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

MQSRKGEGWRDTGTDSLPPFSFCCSPAFSSPLAFGGEGADGCAYILTHVCRYACIAALTLHSEGAERHMRVCVCVRRCAYNEMVLHQVVAFASLAPALHPLSPLPLPCMATTHACCGLRVRSFSLKKSEKKNQQRRLQAPDLSQKTRTRTQKEKQTLQIYLRCVMFKNEYDSDITTWSPTGRLFQIEYANEAVNNGSATVGVKGKNFVVLAALKRSPVAELSSYQEKVFEIDEHVGMSISGLVADGRVLARYLRTECMNYRYMYSNGMPMNQMADMIGEKHQRHIQCSGKRPFGVGLLLAGYDRQGPHLYQTVPSGDVYDYKATAMGVRSQASRTYLERHFEHFSDCTLDELVTHALKALASATSEGIELNVKNTTIAIVGKDTPFTIFEEESARKYLDGFKMRPEDRVAVAEEDEEMLHEQPLDVEE

Entity 7 polymer

描述 description	Proteasome alpha 7 subunit, putative
分子量 formula_weight	25591.8 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

MAGTGSGHDQSTDVFSAEGRVFQVEYAGKAVDNSSTAVAACCKDGVVVAVEKVHTSRMLEKGSNNRIHAVDRQAGICICGLLPDGRAIVSRARQEAENSRDIFATPIRGSVLANRVGEFMHAYTTHFAYRPFGCSAIIASYADDGPQLFVSDPSGTVAGYYGVALGKAKTVAKSELEKLDFSSLTCDEAVGKLASILHEVHDKQKDKLYEVEVAWVCDKSDRKFVHVPADMVPAETSH

Entity 8 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	30280.0 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

MLQRPDHTLLQEPAYPKDIAQKLTENGPAQAGKQLFQPDPAVIDPQLSKAVSLGTTILAVSYNGGVVLAADSRTSSGTYVVNRASNKLTKLTKKIYCCRSGSAADTQALAERVSNYLGSYQTDIGAGVNVATAANLFQKMCYMNRWNISAGIIVAGYDPINGGSVYSIPSGGSCVKLDYALGGSGSIFLYSFFDANYKPGMSKSECVAFCQRAVAHAYSRDGSSGGLIRTITLDADEPEDQTIPWNRSPYCMEKDPKYVTQATQNQPFSSSAKITGNRMSSTG

Entity 9 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	27603.6 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	I,W

MPGFNFENVQRNLNLEGEGYSAPRTLKTGTTIVGVVYRDGVVLGADTRATEGSIVADKRCRKIHYMAPNIMCCGAGTSADTEAVTNMVSSHLALHRLETGKQSRVLEALTLLKRHLYRYQGHVSAALVLGGVDVEGPFLATIAPHGSTDRLPFVTMGSGSIAAMAQLEAAYKDNMTCEEAKELVASAIRKGIFNDPYSGTQVDVCVITKDKTELTIGYDKPNERMYPRQEVLLPPGTTPVLKEEIRQLVDIVDA

Entity 10 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	22470.9 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	J,X

MSIMAYSGGSVMAMAGKECFVIISDNRLGEQLKTISTEVPKLHVVNDSIVYGLTGLRTDQQTFANKVQFRTEMYKLREERDITGKAFAAMITSMLYEARFGPWFVEPVIGSIDKSTGEVYLCATDLIGAPCEPEDYVCAGTAAESLHGMCEALWRPGMSPEELFEIAAQAMLSACDRDSLSGYGAVAMIVTKDKVTTRLIKGRKD

Entity 11 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	23065.3 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	K,Y

MAETAIAFRCKDYVMVAAAGLNAFYYIKITDAEDKITQLDTHQLVACTGENGPRVNFTEYIKCNLALNRMRQHGRHSSCESTANFMRNCLASAIRSREGAYQVNCLFAGYDTPVSEDDDGVVGPQLFYMDYLGTLQAVPYGCHGYGACFVTALLDRLWRPDLSQQEGLELMQKCCDEVKRRVIISNSYFFVKAVTKNGVEVITAVH

Entity 12 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	33576.7 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	L,Z

MFADFEAVTSSNFTLDDCPRVGPFTYHNMDEDTLEEPLSLCSYRRAPQQTDERSPASCDAVTADPLDSSRYLHGENRCWTLKVSCPVPRAIPKLDMKKGTTTLAFRFNGGIIVAVDSRASTGQYIASQTVMKVLEINDYLLGTLAGGAADCQYWERVLGMECRLWELRNGSRITVAAASKILANITYAYRNHGLSMGTMVAGWDQFGPSLYYVDDKGSRVKQDLFSVGSGSIYAYGVLDTGYRKDLSVEDACDLARRSIFHATYRDGASGGIVTVYHVHEKGWTKISRDDQTKLYHRYFPS

Entity 13 polymer

描述 description	Proteasome beta 6 subunit, putative
分子量 formula_weight	37676.9 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	M,a

MASSSPPLLPFSSFVVAVVAIHLSFRVFCVGAQSLCKCCSCVPACALPLCFSSSPSVSAEDVALALFAHPKVLTHRPTARYSPILSLLHYAVMIEDHAEYGHNYYPQKLASSTLTLPQQGAKQQQWSPYQDNGGTTAAIAGKDFVILAGDTRLNGDFCLHSRHDQSKIFQLTPYTYMASNGMQADRLQLQQMLKYRVKWYKYNNGGKVPSTKAIAQLMSTMLYHRRFFPYYTFNMVVGLDEEGHGVCYSYDAVGSTEPFLYGTRGSAASFVEPLLDCLINRQHMTSQAPPEMTKEETLAMLKNAFTGAAERDIYTGDSVSFFIITKDGVQQESFELRKD

Entity 14 polymer

描述 description	Proteasome subunit beta
分子量 formula_weight	24737.2 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	N,b

MASGGSVIAIKYKGGVLMAADTLLSYGSLAKWPNIPRIRLLGSHSAVCATGSYADFQMMAKQVEDNIERQKMYHNVDELSPSEVFSYLHRSIYQKRCDFDPCLCQMVFIGVRDGETFLAGVDDVGTRWEDDCIATGYGAYIALPLLRQALEKNPDGLSRGEAMRILTDCLRVLFYRECRAINKFQVADAASDGVRISEPFDVETHWEYEGYCFEKTAIIR

Entity 15 non-polymer

描述 description	~{N}-[3-(cyclopropylcarbamoyl)phenyl]-6-oxidanylidene-1-(phenylmethyl)pyridazine-3-carboxamide
分子量 formula_weight	388.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

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6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

结构域编号 domain_id	8oluB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	8oluC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	8oluD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	8oluI01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	8oluP01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	8oluQ01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	8oluR01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

结构域编号 domain_id	8oluW01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	60 — 4-Layer Sandwich
拓扑 Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Aminohydrolase, N-terminal nucleophile (Ntn) domain

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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	2.590 Å
最低分辨率 resolution_low	186.180 Å
R 因子 r_factor	0.2490
R_work r_work	0.2490
R_free r_free	—

分辨率 resolution	2.59 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	94595

fit	/app/data/saxs_computation/ol/8olu/8olu.fit
pddf	/app/data/pr_computation/ol/8olu/8olu.pr.out
profile	/app/data/saxs_computation/ol/8olu/8olu.dat

;Leishmania tarentolae proteasome 20S subunit in complex with 1-Benzyl-N-(3-(cyclopropylcarbamoyl)phenyl)-6-oxo-1,6-dihydropyridazine-3-carboxamide ;

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

精修参数 Refinement

冷冻电镜 EM 3D

5. 实体与聚合体信息 (15)

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

6. 折叠分类 (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)