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Crystal structure of the complex of TDP1 with duplex DNA
Analyse Crystal structure of the complex of TDP1 with duplex DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NW9
- Type
- protein + DNA
- Length
- 870 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 1; DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3')
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 431 | 29% helix, 24% strand | Q9NUW8 |
| C | DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3') | dna | 8 | — | — |
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1035 | 0.73 | 0.76 | 88 | empty |
| 2 | 364 | 0.65 | 0.80 | 54 | empty |
| 3 | 162 | 0.49 | 0.78 | 21 | empty |
| 4 | 212 | 0.48 | 0.75 | 33 | empty |
| 5 | 149 | 0.46 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–C · 626 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–B · 598 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9NUW8
- Elsewhere: RCSB PDB 5NW9 · PDBe 5NW9 · UniProt Q9NUW8
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