5vn1

horse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-methylhexylformamide

Method: X-RAY DIFFRACTION Dmax: 117.8 Å Quality: EXCELLENT

1. 蛋白身份与相关结构 Protein Identity & Related Structures

Alcohol dehydrogenase E chain

物种未注明

UniProt P00327

当前结构中的状态

Assembly 聚集状态 构建体 突变与修饰 配体、离子与共同组分 实验方法与环境 结构质量
1 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 A; UniProt 2–375 链 B; UniProt 2–375 未记录 ZN ZINC ION × 4 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 NWH N-[(2S)-heptan-2-yl]formamide × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 X-RAY DIFFRACTION X-ray结晶条件:MICRODIALYSIS;pH 7;278 K;10 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1-methylhexylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25%. Crystal on loop plunged into liquid N2. 分辨率 1.25 Å R-free 0.187
2 蛋白同源多聚体 同源多聚体 蛋白 × 2 PDB 声明:dimeric(2) 与蛋白拷贝数一致 链 C; UniProt 2–375 链 D; UniProt 2–375 未记录 ZN ZINC ION × 4 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 2 NWH N-[(2S)-heptan-2-yl]formamide × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 NMH (R)-N-(1-METHYL-HEXYL)-FORMAMIDE × 1 X-RAY DIFFRACTION X-ray结晶条件:MICRODIALYSIS;pH 7;278 K;10 mg protein/ml dialyzed against 50 mM ammonium N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonate buffer, pH 7 (pH 6.7 at 25 deg C) with 1 mM NADH and 10 mM (racemic) (R,S)-N-1-methylhexylformamide as the concentration of 2-methyl-2,4-pentanediol was raised to 25%. Crystal on loop plunged into liquid N2. 分辨率 1.25 Å R-free 0.187

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly, “相对当前条目”直接指出证据层面的不同;没有差异标签表示当前已读取字段一致。

共 104 个其他 PDB 条目、116 个 assembly。 打开独立比较页并筛选聚集状态

查看构建体与数据证据
UniProt名称 ADH1E_HORSE
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–374; UniProt 2–375 作者链 B; PDB构建体 1–374; UniProt 2–375 作者链 C; PDB构建体 1–374; UniProt 2–375 作者链 D; PDB构建体 1–374; UniProt 2–375

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。 链映射与序列区间收在“数据证据”中;数据库内部编号、导入时间和 assembly 操作表达式仅用于维护,因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

SAXS profile for 5vn1

P(r) 距离分布 P(r) Distribution

P(r) distribution for 5vn1
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id5vn1
沉积日期 deposition_date2017-04-28
结构标题 titlehorse liver alcohol dehydrogenae complexed with NADH (R,S)-N-1-methylhexylformamide
关键词 keywordsoxidoreductase, alcohol dehydrogenase, horse liver, NADH N-1-methylhexylformamide; OXIDOREDUCTASE
实验方法 methodX-RAY DIFFRACTION

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier37.07
回转半径 Rg (电子) rg_electron36.71
零角强度 I(0) i0396693000.00
分子量 molecular_weight163230.0 kDa
排除体积 excluded_volume204980 ų
包络体积 envelope_volume253610 ų
水化壳体积 shell_volume56345 ų
包络直径 envelope_diameter122.5
壳层 Rg shell_rg43.99
包络 Rg envelope_rg36.23
形状 Rg shape_rg36.73
总 Rg total_rg37.10
总原子数 total_atoms11380
残基数 n_residues1496
球谐函数阶数 n_harmonics20
q 范围 q_range— – 0.5000 −1
数据点数 n_points101
壳层类型 shell_typedirectional
溶剂电子密度 solvent_density0.3340 e/ų
壳层衬度 contrast_shell0.0300 e/ų
CRYSOL 版本 crysol_version4.1.3

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax117.8
Rg (实空间) rg_real36.92
Rg 误差 (实空间) rg_real_error1.09
I(0) (实空间) i0_real3.9670e+08
I(0) 误差 (实空间) i0_real_error7.1940e+06
Rg (倒空间) rg_reciprocal37.02
I(0) (倒空间) i0_reciprocal396700000.0000
解质量估计 total_estimate0.9011
解质量评级 solution_quality EXCELLENT a EXCELLENT solution
P(r) 峰数 n_peaks1
主峰位置 r_peak_primary49.3
偏度 Skewness skewness0.159
峰度 Kurtosis kurtosis-0.537
角度范围 angular_range— – 0.2150 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha92760000.0000
实空间数据点数 n_real_points44
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.916

5. 晶体学与实验 5. Crystallography & Experiment

6. 实体与聚合物信息 Entities & Polymers (7)

7. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_idd5vn1a1
类 Class classb — All beta proteins
折叠类型 Fold foldb.35 — GroES-like
超家族 Superfamily superfamilyb.35.1 — GroES-like
家族 Family familyb.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain
结构域编号 domain_idd5vn1a2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain
结构域编号 domain_idd5vn1b1
类 Class classb — All beta proteins
折叠类型 Fold foldb.35 — GroES-like
超家族 Superfamily superfamilyb.35.1 — GroES-like
家族 Family familyb.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain
结构域编号 domain_idd5vn1b2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain
结构域编号 domain_idd5vn1c1
类 Class classb — All beta proteins
折叠类型 Fold foldb.35 — GroES-like
超家族 Superfamily superfamilyb.35.1 — GroES-like
家族 Family familyb.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain
结构域编号 domain_idd5vn1c2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain
结构域编号 domain_idd5vn1d1
类 Class classb — All beta proteins
折叠类型 Fold foldb.35 — GroES-like
超家族 Superfamily superfamilyb.35.1 — GroES-like
家族 Family familyb.35.1.2 — Alcohol dehydrogenase-like, N-terminal domain
结构域编号 domain_idd5vn1d2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
超家族 Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
家族 Family familyc.2.1.1 — Alcohol dehydrogenase-like, C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id5vn1A01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Medium-chain alcohol dehydrogenases, catalytic domain
结构域编号 domain_id5vn1A02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id5vn1B01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Medium-chain alcohol dehydrogenases, catalytic domain
结构域编号 domain_id5vn1B02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id5vn1C01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Medium-chain alcohol dehydrogenases, catalytic domain
结构域编号 domain_id5vn1C02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
结构域编号 domain_id5vn1D01
类 Class class3 — Alpha Beta
架构 Architecture architecture90 — Alpha-Beta Complex
拓扑 Topology topology180 — Quinone Oxidoreductase; Chain A, domain 1
同源超家族 H-superfamily homologous superfamily10 — Medium-chain alcohol dehydrogenases, catalytic domain
结构域编号 domain_id5vn1D02
类 Class class3 — Alpha Beta
架构 Architecture architecture40 — 3-Layer(aba) Sandwich
拓扑 Topology topology50 — Rossmann fold
同源超家族 H-superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain

8. 引用文献 (5)

9. 文件与曲线 (10)