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The crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtg
Analyse The 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
- 1RGU
- Type
- protein + DNA
- Length
- 859 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*GP*TP*G)-3'; Tyrosyl-DNA phosphodiesterase 1
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Ligands
- OTS, SPM, VO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*AP*GP*TP*G)-3' | dna | 3 | — | — |
| F | 5'-D(*AP*GP*TP*G)-3' | dna | 2 | — | — |
| A | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 425 | 28% helix, 24% strand | Q9NUW8 |
| B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 429 | 27% helix, 24% strand | Q9NUW8 |
Ligands and binding sites
- OTS · 4-(2S-amino-1-hydroxyethyl)phenol · ligand · 2 copies · chains D, A, F, B
- SPM · Spermine · ligand · chains A
- VO4 · Vanadate ion · ion · 2 copies · chains D, A, F, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.74 | 0.77 | 105 | empty |
| 2 | 119 | 0.50 | 0.81 | 24 | empty |
| 3 | 107 | 0.36 | 0.74 | 20 | empty |
| 4 | 65 | 0.35 | 0.77 | 21 | empty |
| 5 | 64 | 0.34 | 0.77 | 17 | OTS |
Interfaces
3 interfaces between chains.
- A–B · 599 Ų buried · 4 hydrogen bonds · protein-protein
- D–A · 550 Ų buried · 7 hydrogen bonds · protein-nucleic
- F–B · 439 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 1RGU · The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate… · the same entry in another collection · chain D against D, 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 1RGU · PDBe 1RGU · UniProt Q9NUW8
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