SAXSdb — 1ye3

▼

1. 结构基本信息 1. Structure Basics

条目编号 entry_id	1ye3
沉积日期 deposition_date	2004-12-27
结构标题 title	HORSE LIVER ALCOHOL DEHYDROGENASE APOENZYME
关键词 keywords	DEHYDROGENASE, ALCOHOL, LIVER, APOENZYME, METHYLPENTANEDIOL, OXIDOREDUCTASE; OXIDOREDUCTASE
实验方法 method	X-RAY DIFFRACTION

▼

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	21.88 Å
回转半径 Rg (电子) rg_electron	20.89 Å
零角强度 I(0) i0	26653400.00
分子量 molecular_weight	40057.0 kDa
排除体积 excluded_volume	50457 Å³
包络体积 envelope_volume	58039 Å³
水化壳体积 shell_volume	23196 Å³
包络直径 envelope_diameter	75.9 Å
壳层 Rg shell_rg	27.68 Å
包络 Rg envelope_rg	21.13 Å
形状 Rg shape_rg	20.87 Å
总 Rg total_rg	21.82 Å
总原子数 total_atoms	2795
残基数 n_residues	374
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

▼

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	74.2 Å
Rg (实空间) rg_real	21.85 Å
Rg 误差 (实空间) rg_real_error	0.44 Å
I(0) (实空间) i0_real	2.6650e+07
I(0) 误差 (实空间) i0_real_error	3.7050e+05
Rg (倒空间) rg_reciprocal	21.85 Å
I(0) (倒空间) i0_reciprocal	26650000.0000
解质量估计 total_estimate	0.8745
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	25.5 Å
偏度 Skewness skewness	0.347
峰度 Kurtosis kurtosis	-0.251
角度范围 angular_range	— – 0.3650 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	7587000.0000
实空间数据点数 n_real_points	68
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.999

▶

4. 晶体学与实验 4. Crystallography & Experiment

▶

5. 实体与聚合体信息 (4)

Entity 1 polymer

描述 description	Alcohol dehydrogenase E chain
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	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	2995

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	2

Entity 3 non-polymer

描述 description	(4S)-2-METHYL-2,4-PENTANEDIOL
分子量 formula_weight	118.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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	200

▼

6. 折叠分类 (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

结构域编号 domain_id	d1ye3a1
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	d1ye3a2
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 (2 domains)

结构域编号 domain_id	1ye3A01
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	1ye3A02
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

▶

7. 引用文献 (11)

Horse Liver Alcohol Dehydrogenase Apoenzyme

To be Published

PRIMARY

Amino Acid Residues in the Nicotinamide Binding Site Contribute to Catalysis by Horse Liver Alcohol Dehydrogenase

Biochemistry (2003)

Mobility of Fluorobenzyl Alcohols Bound to Liver Alcohol Dehydrogenases as Determined by NMR and X-Ray Crystallographic Studies

Biochemistry (2002)

Contributions of Valine-292 in the Nicotinamide Binding Site of Liver Alcohol Dehydrogenase and Dynamics to Catalysis

Biochemistry (2001)

;Substitutions in the Flexible Loop of Horse Liver Alcohol Dehydrogenase Hinder the Conformational Change and Unmask Hydrogen Transfer ;

Biochemistry (1999)

Structures of Horse Liver Alcohol Dehydrogenase Complexed with Nad+ and Substituted Benzyl Alcohols

Biochemistry (1994)

Crystallographic Investigations of Nicotinamide Adenine Dinucleotide Binding to Horse Liver Alcohol Dehydrogenase

Biochemistry (1984)

;Crystal Structure Determinations of Coenzyme Analogue and Substrate Complexes of Liver Alcohol Dehydrogenase. Binding of 1,4,5,6-Tetrahydronicotinamide Adenine Dinucleotide and Trans-4-(N,N-Dimethylamino)Cinnamaldehyde to the Enzyme ;

Biochemistry (1982)

Binding of Substrate in a Ternary Complex of Horse Liver Alcohol Dehydrogenase

J.Biol.Chem. (1982)

Structure of a Triclinic Ternary Complex of Horse Liver Alcohol Dehydrogenase at 2.9 Angstroms Resolution

J.Mol.Biol. (1981)

Three-Dimensional Structure of Horse Liver Alcohol Dehydrogenase at 2.4 Angstroms Resolution

J.Mol.Biol. (1976)

▶

晶胞边长 a length_a	55.780 Å
晶胞边长 b length_b	74.290 Å
晶胞边长 c length_c	181.250 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	C 2 2 21
空间群编号 int_tables_number	20
晶系 crystal_system	—

分辨率 resolution	1.590 Å
最低分辨率 resolution_low	20.200 Å
R 因子 r_factor	0.2011
R_work r_work	0.1995
R_free r_free	0.2559

fit	/app/data/saxs_computation/ye/1ye3/1ye3.fit
pddf	/app/data/pr_computation/ye/1ye3/1ye3.pr.out
profile	/app/data/saxs_computation/ye/1ye3/1ye3.dat

HORSE LIVER ALCOHOL DEHYDROGENASE APOENZYME

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