1nop
Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
1. 蛋白身份与相关结构 Protein Identity & Related Structures
当前条目没有可用的 UniProt 蛋白身份。
七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白链接。
当前条目的 assembly 组成
| Assembly | 物理组成 | 蛋白状态 | 蛋白 / DNA / RNA / 其他聚合物 | 数据核对 |
|---|---|---|---|---|
| 1 | 蛋白–DNA | 异源复合物 | 2 / 1 / 0 / 0 | 与全部聚合物一致 |
| 2 | 蛋白–DNA | 单体 | 1 / 1 / 0 / 0 | 与全部聚合物一致 |
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。
2. 结构基本信息 2. Structure Basics
| 条目编号 entry_id | 1nop |
| 沉积日期 deposition_date | 2003-01-16 |
| 结构标题 title | Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide |
| 关键词 keywords | PROTEIN-DNA COMPLEX, vanadate complex, transition state mimic, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA |
| 实验方法 method | X-RAY DIFFRACTION |
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。
1nop__assembly_1__model_1
Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)
1nop__assembly_1__model_1 | I(q)
1nop__assembly_1__model_1 | P(r) · Pending
| Rg（Guinier） | 21.90 Å |
| Rg（电子密度） | 20.66 Å |
| 总 Rg | 21.68 Å |
| 原子数 | 3507 |
| 残基数 | 433 |
| 排除体积 | 62602 ų |
| 最大 q | 0.500 Å⁻¹ |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合物信息 Entities & Polymers (5)
6. 折叠分类 (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| 结构域编号 domain_id | d1nopa1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.136 — Phospholipase D/nuclease |
| 超家族 Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| 家族 Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
| 结构域编号 domain_id | d1nopa2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.136 — Phospholipase D/nuclease |
| 超家族 Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| 家族 Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
| 结构域编号 domain_id | d1nopb1 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.136 — Phospholipase D/nuclease |
| 超家族 Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| 家族 Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
| 结构域编号 domain_id | d1nopb2 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.136 — Phospholipase D/nuclease |
| 超家族 Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| 家族 Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
CATH v4.4 (4 domains)
| 结构域编号 domain_id | 1nopA01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 870 — Endonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Endonuclease Chain A |
| 结构域编号 domain_id | 1nopA02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 870 — Endonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Endonuclease Chain A |
| 结构域编号 domain_id | 1nopB01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 870 — Endonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Endonuclease Chain A |
| 结构域编号 domain_id | 1nopB02 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 30 — 2-Layer Sandwich |
| 拓扑 Topology topology | 870 — Endonuclease; Chain A |
| 同源超家族 H-superfamily homologous superfamily | 10 — Endonuclease Chain A |