1lde

HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL PIPERDINE

Method: X-RAY DIFFRACTION D_max: 223.7 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	1lde
沉积日期 deposition_date	1996-12-25
结构标题 title	HORSE LIVER ALCOHOL DEHYDROGENASE COMPLEXED TO NADH AND N-FORMYL PIPERDINE
关键词 keywords	DEHYDROGENASE, ALCOHOL, NICOTINAMIDE COENZYME, FORMAMIDES, OXIDOREDUCTASE; DEHYDROGENASE
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	72.82 Å
回转半径 Rg (电子) rg_electron	74.67 Å
零角强度 I(0) i0	376729000.00
分子量 molecular_weight	162860.0 kDa
排除体积 excluded_volume	204300 Å³
包络体积 envelope_volume	321250 Å³
水化壳体积 shell_volume	43251 Å³
包络直径 envelope_diameter	253.2 Å
壳层 Rg shell_rg	53.74 Å
包络 Rg envelope_rg	75.08 Å
形状 Rg shape_rg	74.66 Å
总 Rg total_rg	74.17 Å
总原子数 total_atoms	11356
残基数 n_residues	1496
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	223.7 Å
Rg (实空间) rg_real	73.96 Å
Rg 误差 (实空间) rg_real_error	2.35 Å
I(0) (实空间) i0_real	3.7630e+08
I(0) 误差 (实空间) i0_real_error	8.1240e+06
Rg (倒空间) rg_reciprocal	67.41 Å
I(0) (倒空间) i0_reciprocal	371800000.0000
解质量估计 total_estimate	0.5521
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	42.6 Å
偏度 Skewness skewness	0.555
峰度 Kurtosis kurtosis	-1.073
角度范围 angular_range	— – 0.1050 Å⁻¹
当前正则化参数 α current_alpha	0.0016
最高正则化参数 α highest_alpha	5687000.0000
实空间数据点数 n_real_points	22
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.032; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.071; Smooth: 0.017

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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 (5)

Entity 1 polymer

描述 description	LIVER ALCOHOL DEHYDROGENASE
分子量 formula_weight	39853.3 kDa
EC 编号 ec_number	1.1.1.1
来源方法 src_method	nat
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	11912

STAGKVIKCKAAVLWEEKKPFSIEEVEVAPPKAHEVRIKMVATGICRSDDHVVSGTLVTPLPVIAGHEAAGIVESIGEGVTTVRPGDKVIPLFTPQCGKCRVCKHPEGNFCLKNDLSMPRGTMQDGTSRFTCRGKPIHHFLGTSTFSQYTVVDEISVAKIDAASPLEKVCLIGCGFSTGYGSAVKVAKVTQGSTCAVFGLGGVGLSVIMGCKAAGAARIIGVDINKDKFAKAKEVGATECVNPQDYKKPIQEVLTEMSNGGVDFSFEVIGRLDTMVTALSCCQEAYGVSVIVGVPPDSQNLSMNPMLLLSGRTWKGAIFGGFKSKDSVPKLVADFMAKKFALDPLITHVLPFEKINEGFDLLRSGESIRTILTF

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	8

Entity 3 non-polymer

描述 description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
分子量 formula_weight	663.4 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 4 non-polymer

描述 description	N-FORMYLPIPERIDINE
分子量 formula_weight	113.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

Entity 5 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	556

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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	d1ldea1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1ldea2
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1ldeb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1ldeb2
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1ldec1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1ldec2
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

结构域编号 domain_id	d1lded1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.35 — GroES-like
超家族 Superfamily superfamily	b.35.1 — GroES-like
家族 Family family	b.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain

结构域编号 domain_id	d1lded2
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.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	1ldeA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1ldeA02
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	1ldeB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1ldeB02
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	1ldeC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1ldeC02
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	1ldeD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	90 — Alpha-Beta Complex
拓扑 Topology topology	180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily	10 — Medium-chain alcohol dehydrogenases, catalytic domain

结构域编号 domain_id	1ldeD02
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

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7. 引用文献 (5)

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晶胞边长 a length_a	49.930 Å
晶胞边长 b length_b	180.200 Å
晶胞边长 c length_c	86.800 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	106.00 °
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	2.500 Å
最低分辨率 resolution_low	20.000 Å
R 因子 r_factor	—
R_work r_work	0.2050
R_free r_free	0.2560

fit	/app/data/saxs_computation/ld/1lde/1lde.fit
pddf	/app/data/pr_computation/ld/1lde/1lde.pr.out
profile	/app/data/saxs_computation/ld/1lde/1lde.dat