1pl0

Crystal structure of human ATIC in complex with folate-based inhibitor, BW2315U89UC

Method: X-RAY DIFFRACTION D_max: 180.7 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	1pl0
沉积日期 deposition_date	2003-06-06
结构标题 title	Crystal structure of human ATIC in complex with folate-based inhibitor, BW2315U89UC
关键词 keywords	;human ATIC, AICAR, AICAR transformylase, IMP Cyclohydrolase, xanthosine monophosphate, folate-based inhibitor, BW2315U89UC, TRANSFERASE, HYDROLASE ;; TRANSFERASE, 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	54.90 Å
回转半径 Rg (电子) rg_electron	55.52 Å
零角强度 I(0) i0	906399000.00
分子量 molecular_weight	249670.0 kDa
排除体积 excluded_volume	312050 Å³
包络体积 envelope_volume	432340 Å³
水化壳体积 shell_volume	68990 Å³
包络直径 envelope_diameter	193.3 Å
壳层 Rg shell_rg	52.05 Å
包络 Rg envelope_rg	55.33 Å
形状 Rg shape_rg	55.49 Å
总 Rg total_rg	55.50 Å
总原子数 total_atoms	17565
残基数 n_residues	2340
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	180.7 Å
Rg (实空间) rg_real	55.46 Å
Rg 误差 (实空间) rg_real_error	2.33 Å
I(0) (实空间) i0_real	9.0640e+08
I(0) 误差 (实空间) i0_real_error	2.0030e+07
Rg (倒空间) rg_reciprocal	54.40 Å
I(0) (倒空间) i0_reciprocal	905000000.0000
解质量估计 total_estimate	0.5482
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	37.4 Å
偏度 Skewness skewness	0.525
峰度 Kurtosis kurtosis	-0.499
角度范围 angular_range	— – 0.1450 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	85650000.0000
实空间数据点数 n_real_points	30
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.752; Stabil: 1.000; Sysdev: 0.017; Positv: 1.000; Valcen: 0.776; Smooth: 0.038

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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 (6)

Entity 1 polymer

描述 description	Bifunctional purine biosynthesis protein PURH
分子量 formula_weight	64693.7 kDa
EC 编号 ec_number	2.1.2.3, 3.5.4.10
来源方法 src_method	man
拷贝数 entity_count	4

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	17953

MAPGQLALFSVSDKTGLVEFARNLTALGLNLVASGGTAKALRDAGLAVRDVSELTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMARLDFNLIRVVACNLYPFVKTVASPGVTVEEAVEQIDIGGVTLLRAAAKNHARVTVVCEPEDYVVVSTEMQSSESKDTSLETRRQLALKAFTHTAQYDEAISDYFRKQYSKGVSQMPLRYGMNPHQTPAQLYTLQPKLPITVLNGAPGFINLCDALNAWQLVKELKEALGIPAAASFKHVSPAGAAVGIPLSEDEAKVCMVYDLYKTLTPISAAYARARGADRMSSFGDFVALSDVCDVPTAKIISREVSDGIIAPGYEEEALTILSKKKNGNYCVLQMDQSYKPDENEVRTLFGLHLSQKRNNGVVDKSLFSNVVTKNKDLPESALRDLIVATIAVKYTQSNSVCYAKNGQVIGIGAGQQSRIHCTRLAGDKANYWWLRHHPQVLSMKFKTGVKRAEISNAIDQYVTGTIGEDEDLIKWKALFEEVPELLTEAEKKEWVEKLTEVSISSDAFFPFRDNVDRAKRSGVAYIAAPSGSAADKVVIEACDELGIILAHTNLRLFHH

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

Entity 2 non-polymer

描述 description	POTASSIUM ION
分子量 formula_weight	39.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 3 non-polymer

描述 description	XANTHOSINE-5'-MONOPHOSPHATE
分子量 formula_weight	365.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 non-polymer

描述 description	AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE
分子量 formula_weight	338.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

Entity 5 non-polymer

描述 description	N-(4-{[(2-AMINO-4-OXO-3,4-DIHYDROQUINAZOLIN-6-YL)AMINO]SULFONYL}BENZOYL)GLUTAMIC ACID
分子量 formula_weight	489.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 6 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	388

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6. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1pl0a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.24 — Methylglyoxal synthase-like
超家族 Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
家族 Family family	c.24.1.3 — Inosicase

结构域编号 domain_id	d1pl0a2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

结构域编号 domain_id	d1pl0b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.24 — Methylglyoxal synthase-like
超家族 Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
家族 Family family	c.24.1.3 — Inosicase

结构域编号 domain_id	d1pl0b2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

结构域编号 domain_id	d1pl0c1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.24 — Methylglyoxal synthase-like
超家族 Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
家族 Family family	c.24.1.3 — Inosicase

结构域编号 domain_id	d1pl0c2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

结构域编号 domain_id	d1pl0d1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.24 — Methylglyoxal synthase-like
超家族 Superfamily superfamily	c.24.1 — Methylglyoxal synthase-like
家族 Family family	c.24.1.3 — Inosicase

结构域编号 domain_id	d1pl0d2
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.97 — Cytidine deaminase-like
超家族 Superfamily superfamily	c.97.1 — Cytidine deaminase-like
家族 Family family	c.97.1.4 — AICAR transformylase domain of bifunctional purine biosynthesis enzyme ATIC

CATH v4.4 (16 domains)

结构域编号 domain_id	1pl0A01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	440 —

结构域编号 domain_id	1pl0A02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0A03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0A04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

结构域编号 domain_id	1pl0B01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	440 —

结构域编号 domain_id	1pl0B02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0B03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0B04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

结构域编号 domain_id	1pl0C01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	440 —

结构域编号 domain_id	1pl0C02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0C03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0C04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

结构域编号 domain_id	1pl0D01
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	10 — Orthogonal Bundle
拓扑 Topology topology	287 — Helix Hairpins
同源超家族 H-superfamily homologous superfamily	440 —

结构域编号 domain_id	1pl0D02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0D03
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	140 — Cytidine Deaminase; domain 2
同源超家族 H-superfamily homologous superfamily	20 — AICAR transformylase, duplication domain

结构域编号 domain_id	1pl0D04
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily	1380 — Methylglyoxal synthase-like domain

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7. 引用文献 (1)

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晶胞边长 a length_a	77.120 Å
晶胞边长 b length_b	92.970 Å
晶胞边长 c length_c	178.490 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	91.19 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

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	2.600 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2130
R_free r_free	0.2750

fit	/app/data/saxs_computation/pl/1pl0/1pl0.fit
pddf	/app/data/pr_computation/pl/1pl0/1pl0.pr.out
profile	/app/data/saxs_computation/pl/1pl0/1pl0.dat