1w4n

AGAO covalent complex with Tranylcypromine

Method: X-RAY DIFFRACTION Dmax: 106.9 Å Quality: REASONABLE

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

PHENYLETHYLAMINE OXIDASE

ARTHROBACTER GLOBIFORMIS

UniProt P46881

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 3–638 链 B; UniProt 3–638 非标准单体:是(mmCIF未提供具体位点) CU COPPER (II) ION × 2 NA SODIUM ION × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 9 X-RAY DIFFRACTION X-ray结晶条件:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML PROTEIN, 0.05M HEPES, PH 7.0, PLUS 1.5MICROL OF RESERVOIR SOLUTION. A SINGLE CRYSTAL WAS SOAKED WITH TCP BY SLOWLY ADDING TCP TO THE DROP TO ACHIEVE A 100 FOLD EXCESS OF TCP OVER ENZYME ACTIVE SITES. THE CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL, WITH THE CONCENTRAION OF TCP BEING MAINTAINED CONSTANT. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. 分辨率 1.65 Å R-free 0.199

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 105 个其他 PDB 条目、143 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 PAOX_ARTGO
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–636; UniProt 3–638 作者链 B; PDB构建体 1–636; UniProt 3–638

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 1w4n

P(r) 距离分布 P(r) Distribution

P(r) distribution for 1w4n
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2. 结构基本信息 2. Structure Basics

条目编号 entry_id1w4n
沉积日期 deposition_date2004-07-27
结构标题 titleAGAO covalent complex with Tranylcypromine
关键词 keywords;AMINE OXIDASE, ARTHROBACTER GLOBIFORMIS, COPPER CONTAINING, METAL-BINDING, OXIDOREDUCTASE, TCQ, QUINONE, INHIBITED, TCP, TRANYLCYPROMINE ;; 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_guinier32.52
回转半径 Rg (电子) rg_electron31.67
零角强度 I(0) i0305230000.00
分子量 molecular_weight138790.0 kDa
排除体积 excluded_volume172630 ų
包络体积 envelope_volume204460 ų
水化壳体积 shell_volume51846 ų
包络直径 envelope_diameter114.6
壳层 Rg shell_rg40.19
包络 Rg envelope_rg31.94
形状 Rg shape_rg31.65
总 Rg total_rg32.36
总原子数 total_atoms18791
残基数 n_residues1236
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 dmax106.9
Rg (实空间) rg_real32.44
Rg 误差 (实空间) rg_real_error0.81
I(0) (实空间) i0_real3.0520e+08
I(0) 误差 (实空间) i0_real_error5.0030e+06
Rg (倒空间) rg_reciprocal32.47
I(0) (倒空间) i0_reciprocal305200000.0000
解质量估计 total_estimate0.6666
解质量评级 solution_quality REASONABLE a REASONABLE solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary39.3
偏度 Skewness skewness0.346
峰度 Kurtosis kurtosis-0.228
角度范围 angular_range— – 0.2450 −1
当前正则化参数 α current_alpha0.0000
最高正则化参数 α highest_alpha92520000.0000
实空间数据点数 n_real_points50
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.998; Smooth: 0.888

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

6. 实体与聚合物信息 Entities & Polymers (6)

7. 折叠分类 (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

结构域编号 domain_idd1w4na1
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.2 — Amine oxidase catalytic domain
家族 Family familyb.30.2.1 — Amine oxidase catalytic domain
结构域编号 domain_idd1w4na2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.17 — Cystatin-like
超家族 Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
家族 Family familyd.17.2.1 — Amine oxidase N-terminal region
结构域编号 domain_idd1w4na3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.17 — Cystatin-like
超家族 Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
家族 Family familyd.17.2.1 — Amine oxidase N-terminal region
结构域编号 domain_idd1w4nb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.30 — Supersandwich
超家族 Superfamily superfamilyb.30.2 — Amine oxidase catalytic domain
家族 Family familyb.30.2.1 — Amine oxidase catalytic domain
结构域编号 domain_idd1w4nb2
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.17 — Cystatin-like
超家族 Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
家族 Family familyd.17.2.1 — Amine oxidase N-terminal region
结构域编号 domain_idd1w4nb3
类 Class classd — Alpha and beta proteins (a+b)
折叠类型 Fold foldd.17 — Cystatin-like
超家族 Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
家族 Family familyd.17.2.1 — Amine oxidase N-terminal region

CATH v4.4 (6 domains)

结构域编号 domain_id1w4nA01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily40
结构域编号 domain_id1w4nA02
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily40
结构域编号 domain_id1w4nA03
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily20 — Copper amine oxidase, catalytic domain
结构域编号 domain_id1w4nB01
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily40
结构域编号 domain_id1w4nB02
类 Class class3 — Alpha Beta
架构 Architecture architecture10 — Roll
拓扑 Topology topology450 — Nuclear Transport Factor 2; Chain: A,
同源超家族 H-superfamily homologous superfamily40
结构域编号 domain_id1w4nB03
类 Class class2 — Mainly Beta
架构 Architecture architecture70 — Distorted Sandwich
拓扑 Topology topology98 — Beta-galactosidase; Chain A, domain 5
同源超家族 H-superfamily homologous superfamily20 — Copper amine oxidase, catalytic domain

8. 引用文献 (1)

9. 文件与曲线 (10)