1pwu

;Crystal Structure of Anthrax Lethal Factor complexed with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide), a known small molecule inhibitor of matrix metalloproteases. ;

Method: X-RAY DIFFRACTION D_max: 118.0 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	1pwu
沉积日期 deposition_date	2003-07-02
结构标题 title	;Crystal Structure of Anthrax Lethal Factor complexed with (3-(N-hydroxycarboxamido)-2-isobutylpropanoyl-Trp-methylamide), a known small molecule inhibitor of matrix metalloproteases. ;
关键词 keywords	Anthrax Toxin, Lethal Factor, small molecule peptidic inhibitor, hydroxamic acid., hydrolase; HYDROLASE
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	38.43 Å
回转半径 Rg (电子) rg_electron	37.74 Å
零角强度 I(0) i0	439778000.00
分子量 molecular_weight	173340.0 kDa
排除体积 excluded_volume	218240 Å³
包络体积 envelope_volume	296950 Å³
水化壳体积 shell_volume	64376 Å³
包络直径 envelope_diameter	122.2 Å
壳层 Rg shell_rg	44.91 Å
包络 Rg envelope_rg	36.95 Å
形状 Rg shape_rg	37.74 Å
总 Rg total_rg	38.18 Å
总原子数 total_atoms	12238
残基数 n_residues	1483
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	118.0 Å
Rg (实空间) rg_real	38.17 Å
Rg 误差 (实空间) rg_real_error	0.92 Å
I(0) (实空间) i0_real	4.3980e+08
I(0) 误差 (实空间) i0_real_error	7.6050e+06
Rg (倒空间) rg_reciprocal	38.33 Å
I(0) (倒空间) i0_reciprocal	439800000.0000
解质量估计 total_estimate	0.8979
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	51.8 Å
偏度 Skewness skewness	0.111
峰度 Kurtosis kurtosis	-0.509
角度范围 angular_range	— – 0.2050 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	97750000.0000
实空间数据点数 n_real_points	42
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.885

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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	Lethal factor
分子量 formula_weight	90330.8 kDa
EC 编号 ec_number	3.4.24.-
突变 mutation	E720C
来源方法 src_method	man
拷贝数 entity_count	2

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	12238

AGGHGDVGMHVKEKEKNKDENKRKDEERNKTQEEHLKEIMKHIVKIEVKGEEAVKKEAAEKLLEKVPSDVLEMYKAIGGKIYIVDGDITKHISLEALSEDKKKIKDIYGKDALLHEHYVYAKEGYEPVLVIQSSEDYVENTEKALNVYYEIGKILSRDILSKINQPYQKFLDVLNTIKNASDSDGQDLLFTNQLKEHPTDFSVEFLEQNSNEVQEVFAKAFAYYIEPQHRDVLQLYAPEAFNYMDKFNEQEINLSLEELKDQRMLSRYEKWEKIKQHYQHWSDSLSEEGRGLLKKLQIPIEPKKDDIIHSLSQEEKELLKRIQIDSSDFLSTEEKEFLKKLQIDIRDSLSEEEKELLNRIQVDSSNPLSEKEKEFLKKLKLDIQPYDINQRLQDTGGLIDSPSINLDVRKQYKRDIQNIDALLHQSIGSTLYNKIYLYENMNINNLTATLGADLVDSTDNTKINRGIFNEFKKNFKYSISSNYMIVDINERPALDNERLKWRIQLSPDTRAGYLENGKLILQRNIGLEIKDVQIIKQSEKEYIRIDAKVVPKSKIDTKIQEAQLNINQEWNKALGLPKYTKLITFNVHNRYASNIVESAYLILNEWKNNIQSDLIKKVTNYLVDGNGRFVFTDITLPNIAEQYTHQDEIYEQVHSKGLYVPESRSILLHGPSKGVELRNDSEGFIHCFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNEAEFFAEAFRLMHSTDHAERLKVQKNAPKTFQFINDQIKFIINS

来源 Source

来源生物 organism	Bacillus anthracis
NCBI 分类编号 ncbi_taxonomy_id	1392
宿主生物 host_organism	Bacillus anthracis

Entity 2 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	2

Entity 3 non-polymer

描述 description	3-(N-HYDROXYCARBOXAMIDO)-2-ISOBUTYLPROPANOYL-TRP-METHYLAMIDE
分子量 formula_weight	388.5 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) 14 domains

SCOP 2.08 (6 domains)

结构域编号 domain_id	d1pwua1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwua2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwua3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

结构域编号 domain_id	d1pwub1
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwub2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.92 — Zincin-like
超家族 Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
家族 Family family	d.92.1.14 — Anthrax toxin lethal factor, N- and C-terminal domains

结构域编号 domain_id	d1pwub3
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.166 — ADP-ribosylation
超家族 Superfamily superfamily	d.166.1 — ADP-ribosylation
家族 Family family	d.166.1.1 — ADP-ribosylating toxins

CATH v4.4 (8 domains)

结构域编号 domain_id	1pwuA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1pwuA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

结构域编号 domain_id	1pwuA03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2030 — Anthrax toxin lethal factor, domain 3, chain A
同源超家族 H-superfamily homologous superfamily	10 — Anthrax toxin lethal factor, domain 3, chain A

结构域编号 domain_id	1pwuA04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1pwuB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

结构域编号 domain_id	1pwuB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	176 — Toxin ADP-ribosyltransferase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Toxin ADP-ribosyltransferase; Chain A, domain 1

结构域编号 domain_id	1pwuB03
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	2030 — Anthrax toxin lethal factor, domain 3, chain A
同源超家族 H-superfamily homologous superfamily	10 — Anthrax toxin lethal factor, domain 3, chain A

结构域编号 domain_id	1pwuB04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	390 — Collagenase (Catalytic Domain)
同源超家族 H-superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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7. 引用文献 (1)

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晶胞边长 a length_a	96.700 Å
晶胞边长 b length_b	137.400 Å
晶胞边长 c length_c	98.300 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	98.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.700 Å
最低分辨率 resolution_low	33.100 Å
R 因子 r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.2700

fit	/app/data/saxs_computation/pw/1pwu/1pwu.fit
pddf	/app/data/pr_computation/pw/1pwu/1pwu.pr.out
profile	/app/data/saxs_computation/pw/1pwu/1pwu.dat