9ohn

Cryo-EM structure of human p97/VCP bound to inhibitor GND-135

Method: ELECTRON MICROSCOPY D_max: 180.9 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	9ohn
沉积日期 deposition_date	2025-05-05
结构标题 title	Cryo-EM structure of human p97/VCP bound to inhibitor GND-135
关键词 keywords	p97, VCP, TERA, Inhibitor, GND-135, 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	59.26 Å
回转半径 Rg (电子) rg_electron	58.69 Å
零角强度 I(0) i0	15389000000.00
分子量 molecular_weight	683200.0 kDa
排除体积 excluded_volume	654860 Å³
包络体积 envelope_volume	1336500 Å³
水化壳体积 shell_volume	178290 Å³
包络直径 envelope_diameter	178.1 Å
壳层 Rg shell_rg	69.75 Å
包络 Rg envelope_rg	56.61 Å
形状 Rg shape_rg	58.68 Å
总 Rg total_rg	58.83 Å
总原子数 total_atoms	51708
残基数 n_residues	6528
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	180.9 Å
Rg (实空间) rg_real	58.87 Å
Rg 误差 (实空间) rg_real_error	0.94 Å
I(0) (实空间) i0_real	1.5390e+10
I(0) 误差 (实空间) i0_real_error	2.6130e+08
Rg (倒空间) rg_reciprocal	59.57 Å
I(0) (倒空间) i0_reciprocal	15410000000.0000
解质量估计 total_estimate	0.8487
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	76.5 Å
偏度 Skewness skewness	0.111
峰度 Kurtosis kurtosis	-0.507
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	3388000000.0000
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: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.320

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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 (3)

Entity 1 polymer

描述 description	Transitional endoplasmic reticulum ATPase
分子量 formula_weight	91212.6 kDa
EC 编号 ec_number	3.6.4.6
来源方法 src_method	man
拷贝数 entity_count	12

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D,E,F,G,H,I,J,K,L
原子数 atom_count	51708

HHHHHHGTSENLYFQGASGADSKGDDLSTAILKQKNRPNRLIVDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVGYDDIGGCRKQLAQIKEMVELPLRHPALFKAIGVKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDELDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDREVDIGIPDATGRLEILQIHTKNMKLADDVDLEQVANETHGHVGADLAALCSEAALQAIRKKMDLIDLEDETIDAEVMNSLAVTMDDFRWALSQSNPSALRETVVEVPQVTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISIKGPELLTMWFGESEANVREIFDKARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGGTGGSVYTEDNDDDLYG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI 分类编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

描述 description	ADENOSINE-5'-DIPHOSPHATE
分子量 formula_weight	427.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 non-polymer

描述 description	(1P)-1-{4-(benzylamino)-2-methyl-1-[2-(morpholin-4-yl)-2-oxoethyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-2-methyl-1H-indole-4-carboxamide
分子量 formula_weight	536.6 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

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7. 引用文献 (2)

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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	triclinic

分辨率 resolution	2.46 Å
分辨率测定方法 resolution_method	—
颗粒数 num_particles	104767

fit	/app/data/saxs_computation/oh/9ohn/9ohn.fit
pddf	/app/data/pr_computation/oh/9ohn/9ohn.pr.out
profile	/app/data/saxs_computation/oh/9ohn/9ohn.dat