Research workbench
Crystal structure of human tyrosyl-DNA phosphodiesterase (TDP1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide
Analyse Crystal structure of human tyrosyl-DNA phosphodiesterase (TDP1) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NOP
- Type
- protein + DNA
- Length
- 867 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*GP*AP*GP*TP*T)-3'; Tyrosyl-DNA phosphodiesterase 1; Topoisomerase I-derived…
- Ligands
- VO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*AP*GP*AP*GP*TP*T)-3' | dna | 3 | — | — |
| F | 5'-D(*AP*GP*AP*GP*TP*T)-3' | dna | 1 | — | — |
| A | Tyrosyl-DNA phosphodiesterase 1 | protein | 425 | 28% helix, 24% strand | — |
| B | Tyrosyl-DNA phosphodiesterase 1 | protein | 433 | 27% helix, 24% strand | — |
| C | Topoisomerase I-derived peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- VO4 · Vanadate ion · ion · 2 copies · chains D, A, C, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.71 | 0.76 | 86 | empty |
| 2 | 208 | 0.58 | 0.80 | 36 | empty |
| 3 | 106 | 0.47 | 0.80 | 22 | empty |
| 4 | 128 | 0.41 | 0.76 | 22 | empty |
| 5 | 93 | 0.41 | 0.77 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 636 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 597 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 451 Ų buried · 5 hydrogen bonds · protein-protein
- F–B · 272 Ų buried · 4 hydrogen bonds · protein-nucleic
- D–C · 93 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 1NOP · Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate… · the same entry in another collection · chain D against D, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1NOP · PDBe 1NOP
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