3u5z

Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog

Method: X-RAY DIFFRACTION
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1. 蛋白身份与相关结构 Protein Identity & Related Structures

DNA polymerase accessory protein 44

Enterobacteria phage T4

UniProt P04526

当前结构中的状态

Assembly 物理组成 蛋白状态 分子拷贝数 共同组分 数据核对
1 蛋白–DNA 异源复合物 蛋白 8 DNA 2 DNA polymerase accessory protein 62 × 1 (P04527) DNA polymerase processivity component × 3 (P04525) Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 与全部聚合物一致
2 蛋白–DNA 异源复合物 蛋白 8 DNA 2 DNA polymerase accessory protein 62 × 1 (P04527) DNA polymerase processivity component × 3 (P04525) Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 与全部聚合物一致

数据库中的同蛋白其他状态

查看构建体与数据证据
UniProt名称 DPA44_BPT4
Isoform —
PDB实体 1
链与序列区间 作者链 B; PDB构建体 6–324; UniProt 1–319 作者链 C; PDB构建体 6–324; UniProt 1–319 作者链 D; PDB构建体 6–324; UniProt 1–319 作者链 E; PDB构建体 6–324; UniProt 1–319 作者链 L; PDB构建体 6–324; UniProt 1–319 作者链 M; PDB构建体 6–324; UniProt 1–319 作者链 N; PDB构建体 6–324; UniProt 1–319 作者链 O; PDB构建体 6–324; UniProt 1–319

DNA polymerase accessory protein 62

Enterobacteria phage T4

UniProt P04527

当前结构中的状态

Assembly 物理组成 蛋白状态 分子拷贝数 共同组分 数据核对
1 蛋白–DNA 异源复合物 蛋白 8 DNA 2 DNA polymerase accessory protein 44 × 4 (P04526) DNA polymerase processivity component × 3 (P04525) Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 与全部聚合物一致
2 蛋白–DNA 异源复合物 蛋白 8 DNA 2 DNA polymerase accessory protein 44 × 4 (P04526) DNA polymerase processivity component × 3 (P04525) Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 与全部聚合物一致

数据库中的同蛋白其他状态

查看构建体与数据证据
UniProt名称 DPA62_BPT4
Isoform —
PDB实体 2
链与序列区间 作者链 A; PDB构建体 1–186; UniProt 2–187 作者链 K; PDB构建体 1–186; UniProt 2–187

DNA polymerase processivity component

Enterobacteria phage T4

UniProt P04525

当前结构中的状态

Assembly 物理组成 蛋白状态 分子拷贝数 共同组分 数据核对
1 蛋白–DNA 异源复合物 蛋白 8 DNA 2 DNA polymerase accessory protein 44 × 4 (P04526) DNA polymerase accessory protein 62 × 1 (P04527) Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 与全部聚合物一致
2 蛋白–DNA 异源复合物 蛋白 8 DNA 2 DNA polymerase accessory protein 44 × 4 (P04526) DNA polymerase accessory protein 62 × 1 (P04527) Template DNA strand × 1 Primer DNA strand × 1 ;[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium ; × 3 MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 1 与全部聚合物一致

数据库中的同蛋白其他状态

查看构建体与数据证据
UniProt名称 DPA5_BPT4
Isoform —
PDB实体 3
链与序列区间 作者链 F; PDB构建体 1–228; UniProt 1–228 作者链 G; PDB构建体 1–228; UniProt 1–228 作者链 H; PDB构建体 1–228; UniProt 1–228 作者链 P; PDB构建体 1–228; UniProt 1–228 作者链 Q; PDB构建体 1–228; UniProt 1–228 作者链 R; PDB构建体 1–228; UniProt 1–228

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。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id3u5z
沉积日期 deposition_date2011-10-11
结构标题 titleStructure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog
关键词 keywordsAAA+, ATP hydrolase, clamp loader, sliding clamp, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
实验方法 methodX-RAY DIFFRACTION
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3. Official assembly/model 理论 SAXS Official SAXS Profiles

页面只读取最新 assembly 计算结果。每一条曲线都对应明确的 PDB、official biological assembly 和 coordinate model。

3u5z__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

下载该曲线 .dat

3u5z__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 个绘图点;横轴和纵轴均采用对数尺度。

3u5z__assembly_1__model_1 | P(r) · Pending

新版 assembly/model P(r) 尚未计算 此处仅保留位置,不展示旧数据 r (Angstrom) P(r)
P(r) 将按相同 assembly/model 分别计算和展示。
Rg(Guinier)40.85 Å
Rg(电子密度)40.89 Å
总 Rg41.29 Å
原子数17712
残基数2161
排除体积313920 ų
最大 q0.500 Å⁻¹
Assembly Model 结构单元 聚集说明 状态 CRYSOL 操作
1 1 3u5z__assembly_1__model_1 decameric (10) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
2 1 3u5z__assembly_2__model_1 decameric (10) 成功 4.1.3-1-20251215 (887e7ef) 查看 下载
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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合物信息 Entities & Polymers (8)

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6. 折叠分类 (SCOP + CATH) 36 domains

CATH v4.4 (36 domains)

结构域编号 domain_id3u5zA01
类 Class class6 — Special
架构 Architecture architecture10 — Helix non-globular
拓扑 Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily1260 —
结构域编号 domain_id3u5zA02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily50 — Bacteriophage clamp loader A subunit, A' domain
结构域编号 domain_id3u5zA03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily700 — Bacteriophage clamp loader A subunit, A domain
结构域编号 domain_id3u5zB01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zB02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zB03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zC01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zC02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zC03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zD01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zD02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zD03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zE01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zE02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zE03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zF00
类 Class class3 — Alpha Beta
架构 Architecture architecture70 — Box
拓扑 Topology topology10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zG00
类 Class class3 — Alpha Beta
架构 Architecture architecture70 — Box
拓扑 Topology topology10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zH00
类 Class class3 — Alpha Beta
架构 Architecture architecture70 — Box
拓扑 Topology topology10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zK01
类 Class class6 — Special
架构 Architecture architecture10 — Helix non-globular
拓扑 Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
同源超家族 H-superfamily homologous superfamily1260 —
结构域编号 domain_id3u5zK02
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily50 — Bacteriophage clamp loader A subunit, A' domain
结构域编号 domain_id3u5zK03
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily700 — Bacteriophage clamp loader A subunit, A domain
结构域编号 domain_id3u5zL01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zL02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zL03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zM01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zM02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zM03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zN01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zN02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zN03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zO01
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 superfamily300 — P-loop containing nucleotide triphosphate hydrolases
结构域编号 domain_id3u5zO02
类 Class class1 — Mainly Alpha
架构 Architecture architecture10 — Orthogonal Bundle
拓扑 Topology topology8 — Helicase, Ruva Protein; domain 3
同源超家族 H-superfamily homologous superfamily60 —
结构域编号 domain_id3u5zO03
类 Class class1 — Mainly Alpha
架构 Architecture architecture20 — Up-down Bundle
拓扑 Topology topology272 — Zinc Finger, Delta Prime; domain 3
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zP00
类 Class class3 — Alpha Beta
架构 Architecture architecture70 — Box
拓扑 Topology topology10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zQ00
类 Class class3 — Alpha Beta
架构 Architecture architecture70 — Box
拓扑 Topology topology10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily10 —
结构域编号 domain_id3u5zR00
类 Class class3 — Alpha Beta
架构 Architecture architecture70 — Box
拓扑 Topology topology10 — Proliferating Cell Nuclear Antigen
同源超家族 H-superfamily homologous superfamily10 —
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7. 引用文献 (1)