2bgn

HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)

Method: X-RAY DIFFRACTION Dmax: 224.5 Å Quality: GOOD

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

DIPEPTIDYL PEPTIDASE IV

HOMO SAPIENS

UniProt P27487

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 其他组合 异源复合物 蛋白 × 6 其他聚合物 9 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 A; UniProt 39–766 链 B; UniProt 39–766 片段:EXTRACELLULAR DOMAIN, RESIDUES 39-766 ADENOSINE DEAMINASE × 2 (P56658) TAT PROTEIN × 2 (P12506) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2 X-RAY DIFFRACTION mmCIF 未提供已读取环境条件 分辨率 3.15 Å R-free 0.247
2 其他组合 异源复合物 蛋白 × 6 其他聚合物 9 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 C; UniProt 39–766 链 D; UniProt 39–766 片段:EXTRACELLULAR DOMAIN, RESIDUES 39-766 ADENOSINE DEAMINASE × 2 (P56658) TAT PROTEIN × 2 (P12506) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2 X-RAY DIFFRACTION mmCIF 未提供已读取环境条件 分辨率 3.15 Å R-free 0.247

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 113 个其他 PDB 条目、168 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 DPP4_HUMAN
Isoform
PDB实体 1
链与序列区间 作者链 A; PDB构建体 1–728; UniProt 39–766 作者链 B; PDB构建体 1–728; UniProt 39–766 作者链 C; PDB构建体 1–728; UniProt 39–766 作者链 D; PDB构建体 1–728; UniProt 39–766

ADENOSINE DEAMINASE

物种未注明

UniProt P56658

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 其他组合 异源复合物 蛋白 × 6 其他聚合物 9 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 E; UniProt 1–362 链 F; UniProt 1–362 未记录 DIPEPTIDYL PEPTIDASE IV × 2 (P27487) TAT PROTEIN × 2 (P12506) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2 X-RAY DIFFRACTION mmCIF 未提供已读取环境条件 分辨率 3.15 Å R-free 0.247
2 其他组合 异源复合物 蛋白 × 6 其他聚合物 9 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 G; UniProt 1–362 链 H; UniProt 1–362 未记录 DIPEPTIDYL PEPTIDASE IV × 2 (P27487) TAT PROTEIN × 2 (P12506) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2 X-RAY DIFFRACTION mmCIF 未提供已读取环境条件 分辨率 3.15 Å R-free 0.247

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 16 个其他 PDB 条目、17 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 ADA_BOVIN
Isoform
PDB实体 2
链与序列区间 作者链 E; PDB构建体 2–363; UniProt 1–362 作者链 F; PDB构建体 2–363; UniProt 1–362 作者链 G; PDB构建体 2–363; UniProt 1–362 作者链 H; PDB构建体 2–363; UniProt 1–362

TAT PROTEIN

物种未注明

UniProt P12506

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 其他组合 异源复合物 蛋白 × 6 其他聚合物 9 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 W; UniProt 1–9 链 X; UniProt 1–9 片段:HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE, RESIDUES 1-9 突变:YES DIPEPTIDYL PEPTIDASE IV × 2 (P27487) ADENOSINE DEAMINASE × 2 (P56658) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2 X-RAY DIFFRACTION mmCIF 未提供已读取环境条件 分辨率 3.15 Å R-free 0.247
2 其他组合 异源复合物 蛋白 × 6 其他聚合物 9 PDB 声明:hexameric(6) 与蛋白拷贝数一致 链 Y; UniProt 1–9 链 Z; UniProt 1–9 片段:HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE, RESIDUES 1-9 突变:YES DIPEPTIDYL PEPTIDASE IV × 2 (P27487) ADENOSINE DEAMINASE × 2 (P56658) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 2 X-RAY DIFFRACTION mmCIF 未提供已读取环境条件 分辨率 3.15 Å R-free 0.247

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 6 个其他 PDB 条目、7 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 TAT_HV1Z2
Isoform
PDB实体 3
链与序列区间 作者链 W; PDB构建体 1–9; UniProt 1–9 作者链 X; PDB构建体 1–9; UniProt 1–9 作者链 Y; PDB构建体 1–9; UniProt 1–9 作者链 Z; PDB构建体 1–9; UniProt 1–9

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 2bgn

P(r) 距离分布 P(r) Distribution

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

条目编号 entry_id2bgn
沉积日期 deposition_date2005-01-03
结构标题 titleHIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)
关键词 keywords;HYDROLASE, HYDROLASE-COMPLEX, DIPETIDYL PEPTIDASE IV, DPPIV, CD26, ALPHA/BETA-HYDROLASE FOLD, BETA-PROPELLER FOLD, PROTEIN-PROTEIN COMPLEX, ADENOSINE DEAMINASE, ADA, SERINE PROTEASE, AMINOPEPTIDASE, HIV-1 TAT PROTEIN ;; HYDROLASE
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_guinier75.42
回转半径 Rg (电子) rg_electron76.16
零角强度 I(0) i03601120000.00
分子量 molecular_weight511740.0 kDa
排除体积 excluded_volume640730 ų
包络体积 envelope_volume1005600 ų
水化壳体积 shell_volume117260 ų
包络直径 envelope_diameter264.6
壳层 Rg shell_rg65.83
包络 Rg envelope_rg74.65
形状 Rg shape_rg76.13
总 Rg total_rg76.11
总原子数 total_atoms36096
残基数 n_residues4344
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 dmax224.5
Rg (实空间) rg_real75.18
Rg 误差 (实空间) rg_real_error1.52
I(0) (实空间) i0_real3.5840e+09
I(0) 误差 (实空间) i0_real_error7.6160e+07
Rg (倒空间) rg_reciprocal73.03
I(0) (倒空间) i0_reciprocal3579000000.0000
解质量估计 total_estimate0.8469
解质量评级 solution_quality GOOD a GOOD solution
P(r) 峰数 n_peaks2
主峰位置 r_peak_primary64.1
偏度 Skewness skewness0.518
峰度 Kurtosis kurtosis-0.443
角度范围 angular_range— – 0.1050 −1
当前正则化参数 α current_alpha0.0177
最高正则化参数 α highest_alpha89350000.0000
实空间数据点数 n_real_points22
GNOM 版本 gnom_version4.1.3
质量判据 quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 0.993; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.299

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

6. 实体与聚合物信息 Entities & Polymers (9)

7. 折叠分类 (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

结构域编号 domain_idd2bgna1
类 Class classb — All beta proteins
折叠类型 Fold foldb.70 — 8-bladed beta-propeller
超家族 Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
家族 Family familyb.70.3.1 — DPP6 N-terminal domain-like
结构域编号 domain_idd2bgna2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
家族 Family familyc.69.1.24 — DPP6 catalytic domain-like
结构域编号 domain_idd2bgnb1
类 Class classb — All beta proteins
折叠类型 Fold foldb.70 — 8-bladed beta-propeller
超家族 Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
家族 Family familyb.70.3.1 — DPP6 N-terminal domain-like
结构域编号 domain_idd2bgnb2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
家族 Family familyc.69.1.24 — DPP6 catalytic domain-like
结构域编号 domain_idd2bgnc1
类 Class classb — All beta proteins
折叠类型 Fold foldb.70 — 8-bladed beta-propeller
超家族 Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
家族 Family familyb.70.3.1 — DPP6 N-terminal domain-like
结构域编号 domain_idd2bgnc2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
家族 Family familyc.69.1.24 — DPP6 catalytic domain-like
结构域编号 domain_idd2bgnd1
类 Class classb — All beta proteins
折叠类型 Fold foldb.70 — 8-bladed beta-propeller
超家族 Superfamily superfamilyb.70.3 — DPP6 N-terminal domain-like
家族 Family familyb.70.3.1 — DPP6 N-terminal domain-like
结构域编号 domain_idd2bgnd2
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.69 — alpha/beta-Hydrolases
超家族 Superfamily superfamilyc.69.1 — alpha/beta-Hydrolases
家族 Family familyc.69.1.24 — DPP6 catalytic domain-like
结构域编号 domain_idd2bgne1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
家族 Family familyc.1.9.1 — Adenosine/AMP deaminase
结构域编号 domain_idd2bgnf1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
家族 Family familyc.1.9.1 — Adenosine/AMP deaminase
结构域编号 domain_idd2bgng1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
家族 Family familyc.1.9.1 — Adenosine/AMP deaminase
结构域编号 domain_idd2bgnh1
类 Class classc — Alpha and beta proteins (a/b)
折叠类型 Fold foldc.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamilyc.1.9 — Metallo-dependent hydrolases
家族 Family familyc.1.9.1 — Adenosine/AMP deaminase

CATH v4.4 (12 domains)

结构域编号 domain_id2bgnA01
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 superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
结构域编号 domain_id2bgnA02
类 Class class2 — Mainly Beta
架构 Architecture architecture140 — 8 Propeller
拓扑 Topology topology10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
结构域编号 domain_id2bgnB01
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 superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
结构域编号 domain_id2bgnB02
类 Class class2 — Mainly Beta
架构 Architecture architecture140 — 8 Propeller
拓扑 Topology topology10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
结构域编号 domain_id2bgnC01
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 superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
结构域编号 domain_id2bgnC02
类 Class class2 — Mainly Beta
架构 Architecture architecture140 — 8 Propeller
拓扑 Topology topology10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
结构域编号 domain_id2bgnD01
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 superfamily1820 — Alpha/Beta hydrolase fold, catalytic domain
结构域编号 domain_id2bgnD02
类 Class class2 — Mainly Beta
架构 Architecture architecture140 — 8 Propeller
拓扑 Topology topology10 — Methanol Dehydrogenase; Chain A
同源超家族 H-superfamily homologous superfamily30 — Dipeptidylpeptidase IV, N-terminal domain
结构域编号 domain_id2bgnE00
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily140 — Metal-dependent hydrolases
结构域编号 domain_id2bgnF00
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily140 — Metal-dependent hydrolases
结构域编号 domain_id2bgnG00
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily140 — Metal-dependent hydrolases
结构域编号 domain_id2bgnH00
类 Class class3 — Alpha Beta
架构 Architecture architecture20 — Alpha-Beta Barrel
拓扑 Topology topology20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily140 — Metal-dependent hydrolases

8. 引用文献 (1)

9. 文件与曲线 (10)