8ez4

Plasmodium falciparum M17 in complex with inhibitor 9aa

Method: X-RAY DIFFRACTION D_max: 211.3 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	8ez4
沉积日期 deposition_date	2022-10-31
结构标题 title	Plasmodium falciparum M17 in complex with inhibitor 9aa
关键词 keywords	Malaria, metalloaminopeptidase, inhibitor complex, HYDROLASE, HYDROLASE-HYDROLASE inhibitor complex; HYDROLASE/HYDROLASE inhibitor
实验方法 method	X-RAY DIFFRACTION

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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	71.71 Å
回转半径 Rg (电子) rg_electron	71.97 Å
零角强度 I(0) i0	6189480000.00
分子量 molecular_weight	687420.0 kDa
排除体积 excluded_volume	866400 Å³
包络体积 envelope_volume	1168400 Å³
水化壳体积 shell_volume	133710 Å³
包络直径 envelope_diameter	243.4 Å
壳层 Rg shell_rg	71.04 Å
包络 Rg envelope_rg	70.55 Å
形状 Rg shape_rg	72.00 Å
总 Rg total_rg	71.88 Å
总原子数 total_atoms	48306
残基数 n_residues	6232
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	211.3 Å
Rg (实空间) rg_real	71.59 Å
Rg 误差 (实空间) rg_real_error	1.17 Å
I(0) (实空间) i0_real	6.1700e+09
I(0) 误差 (实空间) i0_real_error	1.2670e+08
Rg (倒空间) rg_reciprocal	70.46 Å
I(0) (倒空间) i0_reciprocal	6170000000.0000
解质量估计 total_estimate	0.8054
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	57.6 Å
偏度 Skewness skewness	0.388
峰度 Kurtosis kurtosis	-0.732
角度范围 angular_range	— – 0.1100 Å⁻¹
当前正则化参数 α current_alpha	0.0225
最高正则化参数 α highest_alpha	1925000000.0000
实空间数据点数 n_real_points	23
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.831; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.001

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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 (9)

Entity 1 polymer

描述 description	M17 leucyl aminopeptidase
分子量 formula_weight	58577.8 kDa
EC 编号 ec_number	3.4.11.1
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	53046

ASEVPQVVSLDPTSIPIEYNTPIHDIKVQVYDIKGGCNVEEGLTIFLVNNPGKENGPVKISSKVNDKQVSEFLKDENMEKFNVKLGTSKHFYMFNDNKNSVAVGYVGCGSVADLSEADMKRVVLSLVTMLHDNKLSKLTVVFEINVDKNLFRFFLETLFYEYMTDERFKSTDKNVNMEYIKHLGVYINNADTYKEEVEKARVYYFGTYYASQLIAAPSNYCNPVSLSNAAVELAQKLNLEYKILGVKELEELKMGAYLSVGKGSMYPNKFIHLTYKSKGDVKKKIALVGKGITFDSGGYNLKAAPGSMIDLMKFDMSGCAAVLGCAYCVGTLKPENVEIHFLSAVCENMVSKNSYRPGDIITASNGKTIEVGNTDAEGRLTLADALVYAEKLGVDYIVDIATLTGAMLYSLGTSYAGVFGNNEELINKILQSSKTSNEPVWWLPIINEYRATLNSKYADINQISSSVKASSIVASLFLKEFVQNTAWAHIDIAGVSWNFKARKPKGFGVRLLTEFVLNDALHHHHHH

来源 Source

来源生物 organism	Plasmodium falciparum
通用名 common_name	malaria parasite P. falciparum
NCBI 分类编号 ncbi_taxonomy_id	5833
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	N-[(1R)-2-(hydroxyamino)-2-oxo-1-(3',4',5'-trifluoro[1,1'-biphenyl]-4-yl)ethyl]-N~2~-phenylglycinamide
分子量 formula_weight	429.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 3 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	13

Entity 4 non-polymer

描述 description	PENTAETHYLENE GLYCOL
分子量 formula_weight	238.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	30

Entity 5 non-polymer

描述 description	CARBONATE ION
分子量 formula_weight	60.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	12

Entity 6 non-polymer

描述 description	ZINC ION
分子量 formula_weight	65.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	24

Entity 7 non-polymer

描述 description	SODIUM ION
分子量 formula_weight	23.0 kDa
来源方法 src_method	syn
拷贝数 entity_count	9

Entity 8 non-polymer

描述 description	NONAETHYLENE GLYCOL
分子量 formula_weight	414.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 9 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	4701

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6. 折叠分类 (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

结构域编号 domain_id	8ez4A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4C01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4D01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4E01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4E02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4F01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4F02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4G01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4G02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4H01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4H02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4I01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4I02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4J01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4J02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4K01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4K02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

结构域编号 domain_id	8ez4L01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	220 — Leucine Aminopeptidase, subunit E; domain 1
同源超家族 H-superfamily homologous superfamily	10 — Leucine Aminopeptidase, subunit E, domain 1

结构域编号 domain_id	8ez4L02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	630 — Aminopeptidase
同源超家族 H-superfamily homologous superfamily	10 — Zn peptidases

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7. 引用文献 (1)

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晶胞边长 a length_a	173.940 Å
晶胞边长 b length_b	176.600 Å
晶胞边长 c length_c	230.901 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	48

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	1.890 Å
最低分辨率 resolution_low	48.470 Å
R 因子 r_factor	0.1793
R_work r_work	0.1774
R_free r_free	0.2164

fit	/app/data/saxs_computation/ez/8ez4/8ez4.fit
pddf	/app/data/pr_computation/ez/8ez4/8ez4.pr.out
profile	/app/data/saxs_computation/ez/8ez4/8ez4.dat