1k3t

;Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi Complexed with Chalepin, a Coumarin Derivative Inhibitor ;

Method: X-RAY DIFFRACTION D_max: 102.2 Å Quality: EXCELLENT

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	1k3t
沉积日期 deposition_date	2001-10-04
结构标题 title	;Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi Complexed with Chalepin, a Coumarin Derivative Inhibitor ;
关键词 keywords	Apo-Protein, gGAPDH-Chalepin complex, glycosome, Trypanosoma cruzi, OXIDOREDUCTASE; OXIDOREDUCTASE
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	33.79 Å
回转半径 Rg (电子) rg_electron	32.89 Å
零角强度 I(0) i0	381955000.00
分子量 molecular_weight	156510.0 kDa
排除体积 excluded_volume	195590 Å³
包络体积 envelope_volume	235620 Å³
水化壳体积 shell_volume	56683 Å³
包络直径 envelope_diameter	107.7 Å
壳层 Rg shell_rg	41.90 Å
包络 Rg envelope_rg	32.86 Å
形状 Rg shape_rg	32.87 Å
总 Rg total_rg	33.59 Å
总原子数 total_atoms	10999
残基数 n_residues	1436
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	102.2 Å
Rg (实空间) rg_real	33.57 Å
Rg 误差 (实空间) rg_real_error	0.46 Å
I(0) (实空间) i0_real	3.8200e+08
I(0) 误差 (实空间) i0_real_error	5.6180e+06
Rg (倒空间) rg_reciprocal	33.71 Å
I(0) (倒空间) i0_reciprocal	382000000.0000
解质量估计 total_estimate	0.9035
解质量评级 solution_quality	EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	45.6 Å
偏度 Skewness skewness	0.047
峰度 Kurtosis kurtosis	-0.557
角度范围 angular_range	— – 0.2350 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	153300000.0000
实空间数据点数 n_real_points	48
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.964

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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	Glyceraldehyde-3-phosphate dehydrogenase
分子量 formula_weight	39112.5 kDa
EC 编号 ec_number	1.2.1.12
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	11942

MPIKVGINGFGRIGRMVFQALCEDGLLGTEIDVVAVVDMNTDAEYFAYQMRYDTVHGKFKYEVTTTKSSPSVAKDDTLVVNGHRILCVKAQRNPADLPWGKLGVEYVIESTGLFTAKAAAEGHLRGGARKVVISAPASGGAKTLVMGVNHHEYNPSEHHVVSNASCTTNCLAPIVHVLVKEGFGVQTGLMTTIHSYTATQKTVDGVSVKDWRGGRAAAVNIIPSTTGAAKAVGMVIPSTQGKLTGMSFRVPTPDVSVVDLTFTAARDTSIQEIDAALKRASKTYMKGILGYTDEELVSADFINDNRSSIYDSKATLQNNLPKERRFFKIVSWYDNEWGYSHRVVDLVRHMASKDRSARL

来源 Source

来源生物 organism	Trypanosoma cruzi
NCBI 分类编号 ncbi_taxonomy_id	5693
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	6-(1,1-DIMETHYLALLYL)-2-(1-HYDROXY-1-METHYLETHYL)-2,3-DIHYDRO-7H-FURO[3,2-G]CHROMEN-7-ONE
分子量 formula_weight	314.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

Entity 3 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	937

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6. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d1k3ta1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1k3ta2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.1 — GAPDH-like

结构域编号 domain_id	d1k3tb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1k3tb2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.1 — GAPDH-like

结构域编号 domain_id	d1k3tc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1k3tc2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.1 — GAPDH-like

结构域编号 domain_id	d1k3td1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family family	c.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1k3td2
类 Class class	d — Alpha and beta proteins (a+b)
折叠类型 Fold fold	d.81 — FwdE/GAPDH domain-like
超家族 Superfamily superfamily	d.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
家族 Family family	d.81.1.1 — GAPDH-like

CATH v4.4 (8 domains)

结构域编号 domain_id	1k3tA01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1k3tA02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1k3tB01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1k3tB02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1k3tC01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1k3tC02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

结构域编号 domain_id	1k3tD01
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	720 — NAD(P)-binding Rossmann-like Domain

结构域编号 domain_id	1k3tD02
类 Class class	3 — Alpha Beta
架构 Architecture architecture	30 — 2-Layer Sandwich
拓扑 Topology topology	360 — Dihydrodipicolinate Reductase; domain 2
同源超家族 H-superfamily homologous superfamily	10 — Dihydrodipicolinate Reductase; domain 2

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7. 引用文献 (3)

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晶胞边长 a length_a	82.080 Å
晶胞边长 b length_b	84.970 Å
晶胞边长 c length_c	105.240 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	96.32 °
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	1.950 Å
最低分辨率 resolution_low	15.000 Å
R 因子 r_factor	—
R_work r_work	0.2010
R_free r_free	0.2800

fit	/app/data/saxs_computation/k3/1k3t/1k3t.fit
pddf	/app/data/pr_computation/k3/1k3t/1k3t.pr.out
profile	/app/data/saxs_computation/k3/1k3t/1k3t.dat