Research workbench
Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC
Analyse Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RFI
- Type
- protein + DNA
- Length
- 868 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- 5'-D(*AP*GP*TP*C)-3'; Tyrosyl-DNA phosphodiesterase 1; Topoisomerase I-Derived Peptide
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Ligands
- SPM, VO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.2 · 5 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | 5'-D(*AP*GP*TP*C)-3' | dna | 3 | — | — |
| A | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 425 | 29% helix, 25% strand | Q9NUW8 |
| B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 429 | 28% helix, 24% strand | Q9NUW8 |
| C | Topoisomerase I-Derived Peptide | protein | 5 | 0% helix, 0% strand | — |
| E | Topoisomerase I-Derived Peptide | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.74 | 0.77 | 103 | empty |
| 2 | 104 | 0.49 | 0.81 | 24 | empty |
| 3 | 152 | 0.46 | 0.76 | 24 | empty |
| 4 | 105 | 0.39 | 0.76 | 19 | empty |
| 5 | 73 | 0.36 | 0.77 | 22 | empty |
Interfaces
7 interfaces between chains.
- A–B · 591 Ų buried · 3 hydrogen bonds · protein-protein
- F–B · 539 Ų buried · 10 hydrogen bonds · protein-nucleic
- D–A · 538 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 493 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 326 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1RFI · Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9NUW8 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 1 (Q9NUW8) · a predicted model of the same protein · chain A against A, 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
- Every structure of UniProt Q9NUW8
- Elsewhere: RCSB PDB 1RFI · PDBe 1RFI · UniProt Q9NUW8
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