1nop
Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
1. Protein Identity and Related Structures Protein Identity & Related Structures
No usable UniProt protein identity is available for this entry.
The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.
Assembly Composition of the Current Entry
| Assembly | Physical composition | Protein state | 蛋白 / DNA / RNA / 其他Polymer | Data consistency |
|---|---|---|---|---|
| 1 | Protein–DNA | Heteromer | 2 / 1 / 0 / 0 | Consistent with all polymers |
| 2 | Protein–DNA | Monomer | 1 / 1 / 0 / 0 | Consistent with all polymers |
The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.
2. Structure Basics 2. Structure Basics
| Entry ID entry_id | 1nop |
| Deposition date deposition_date | 2003-01-16 |
| Structure title title | Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide |
| Keywords keywords | PROTEIN-DNA COMPLEX, vanadate complex, transition state mimic, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA |
| Experimental Method method | X-RAY DIFFRACTION |
3. Official assembly/model SAXS Official SAXS Profiles
This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and 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 (electron density) | 20.66 Å |
| Total Rg | 21.68 Å |
| Atom count | 3507 |
| Residues | 433 |
| Excluded volume | 62602 ų |
| Maximum q | 0.500 Å⁻¹ |
4. Crystallography and Experiment 4. Crystallography & Experiment
5. Entities and Polymers Entities & Polymers (5)
6. Fold Classification (SCOP + CATH) 8 domains
SCOP 2.08 (4 domains)
| Domain ID domain_id | d1nopa1 |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.136 — Phospholipase D/nuclease |
| Superfamily Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| Family Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
| Domain ID domain_id | d1nopa2 |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.136 — Phospholipase D/nuclease |
| Superfamily Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| Family Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
| Domain ID domain_id | d1nopb1 |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.136 — Phospholipase D/nuclease |
| Superfamily Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| Family Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
| Domain ID domain_id | d1nopb2 |
| Class class | d — Alpha and beta proteins (a+b) |
| Fold Fold fold | d.136 — Phospholipase D/nuclease |
| Superfamily Superfamily superfamily | d.136.1 — Phospholipase D/nuclease |
| Family Family family | d.136.1.3 — Tyrosyl-DNA phosphodiesterase TDP1 |
CATH v4.4 (4 domains)
| Domain ID domain_id | 1nopA01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 870 — Endonuclease; Chain A |
| Homologous superfamily homologous superfamily | 10 — Endonuclease Chain A |
| Domain ID domain_id | 1nopA02 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 870 — Endonuclease; Chain A |
| Homologous superfamily homologous superfamily | 10 — Endonuclease Chain A |
| Domain ID domain_id | 1nopB01 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 870 — Endonuclease; Chain A |
| Homologous superfamily homologous superfamily | 10 — Endonuclease Chain A |
| Domain ID domain_id | 1nopB02 |
| Class class | 3 — Alpha Beta |
| Architecture architecture | 30 — 2-Layer Sandwich |
| Topology topology | 870 — Endonuclease; Chain A |
| Homologous superfamily homologous superfamily | 10 — Endonuclease Chain A |