SAXSdb — 1thz

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1thz
沉积日期 deposition_date	2004-06-01
结构标题 title	Crystal Structure of Avian AICAR Transformylase in Complex with a Novel Inhibitor Identified by Virtual Ligand Screening
关键词 keywords	ATIC, Virtual Ligand Screening, Purine biosynthesis, Cancer Target, 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	34.34 Å
回转半径 Rg (电子) rg_electron	33.83 Å
零角强度 I(0) i0	258084000.00
分子量 molecular_weight	129360.0 kDa
排除体积 excluded_volume	162050 Å³
包络体积 envelope_volume	201440 Å³
水化壳体积 shell_volume	49073 Å³
包络直径 envelope_diameter	114.0 Å
壳层 Rg shell_rg	41.08 Å
包络 Rg envelope_rg	33.99 Å
形状 Rg shape_rg	33.82 Å
总 Rg total_rg	34.38 Å
总原子数 total_atoms	9090
残基数 n_residues	1180
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	112.4 Å
Rg (实空间) rg_real	34.38 Å
Rg 误差 (实空间) rg_real_error	0.78 Å
I(0) (实空间) i0_real	2.5810e+08
I(0) 误差 (实空间) i0_real_error	4.6510e+06
Rg (倒空间) rg_reciprocal	34.36 Å
I(0) (倒空间) i0_reciprocal	258100000.0000
解质量估计 total_estimate	0.8858
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	36.7 Å
偏度 Skewness skewness	0.373
峰度 Kurtosis kurtosis	-0.479
角度范围 angular_range	— – 0.2300 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	101300000.0000
实空间数据点数 n_real_points	47
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.929

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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 (4)

Entity 1 polymer

描述 description	Bifunctional purine biosynthesis protein PURH
分子量 formula_weight	64497.7 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	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	9838

MAARQQLALLSVSEKAGLVEFARSLNALGLGLIASGGTATALRDAGLPVRDVSDLTGFPEMLGGRVKTLHPAVHAGILARNIPEDNADMNKQDFSLVRVVVCNLYPFVKTVSSPGVTVPEAVEKIDIGGVALLRAAAKNHARVTVVCDPADYSSVAKEMAASKDKDTSVETRRHLALKAFTHTAQYDAAISDYFRKEYSKGVSQLPLRYGMNPHQSPAQLYTTRPKLPLTVVNGSPGFINLCDALNAWQLVKELKQALGIPAAASFKHVSPAGAAVGIPLSEEEAQVCMVHDLHKTLTPLASAYARSRGADRMSSFGDFIALSDICDVPTAKIISREVSDGVVAPGYEEEALKILSKKKNGGYCVLQMDPNYEPDDNEIRTLYGLQLMQKRNNAVIDRSLFKNIVTKNKTLPESAVRDLIVASIAVKYTQSNSVCYAKDGQVIGIGAGQQSRIHCTRLAGDKANSWWLRHHPRVLSMKFKAGVKRAEVSNAIDQYVTGTIGEDEDLVKWQAMFEEVPAQLTEAEKKQWIAKLTAVSLSSDAFFPFRDNVDRAKRIGVQFIVAPSGSAADEVVIEACNELGITLIHTNLRLFHH

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI 分类编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli BL21(DE3)

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	2

Entity 3 non-polymer

描述 description	2-{(E)-[5-HYDROXY-3-METHYL-1-(2-METHYL-4-SULFOPHENYL)-1H-PYRAZOL-4-YL]DIAZENYL}-4-SULFOBENZOIC ACID
分子量 formula_weight	496.5 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

Entity 4 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	748

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6. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d1thza1
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	d1thza2
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	d1thzb1
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	d1thzb2
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 (8 domains)

结构域编号 domain_id	1thzA01
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	1thzA02
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	1thzA03
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	1thzA04
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	1thzB01
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	1thzB02
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	1thzB03
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	1thzB04
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 (6)

;Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening. ;

J.Biol.Chem. (2004)

PMID: 15355974 · DOI: 10.1074/jbc.M406801200 PRIMARY

Structural Insights Into the Human and Avian Imp Cyclohydrolase Mechanism Via Crystal Structures with the Bound Xmp Inhibitor

Biochemistry (2004)

PMID: 14756553 · DOI: 10.1021/bi030162i

;Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates. ;

J.Biol.Chem. (2004)

PMID: 14966129 · DOI: 10.1074/jbc.M313691200

Structure of Avian Aicar Transformylase with a Multisubstrate Adduct Inhibitor Beta-Dadf Identifies the Folate Binding Site

Biochemistry (2003)

PMID: 12974624 · DOI: 10.1021/bi030106h

Structural Insights Into the Avian Aicar Transformylase Mechanism

Biochemistry (2002)

PMID: 12501179 · DOI: 10.1021/bi020505x

Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis.

Nat.Struct.Mol.Biol. (2001)

DOI: 10.1038/87555

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晶胞边长 a length_a	64.800 Å
晶胞边长 b length_b	105.300 Å
晶胞边长 c length_c	102.400 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	108.10 °
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	1.800 Å
最低分辨率 resolution_low	31.010 Å
R 因子 r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2400

fit	/app/data/saxs_computation/th/1thz/1thz.fit
pddf	/app/data/pr_computation/th/1thz/1thz.pr.out
profile	/app/data/saxs_computation/th/1thz/1thz.dat

Crystal Structure of Avian AICAR Transformylase in Complex with a Novel Inhibitor Identified by Virtual Ligand Screening

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

衍射实验 Diffraction