MolNFT v1 · #20478 · protein + DNA
Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide agtt
1RG1 · 5'-D(*AP*GP*TP*T)-3': “Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octopamine, and…”. X-ray diffraction, 3 ligands (OTS, SPM, VO4), 5 pockets (best druggability 0.70). MolNFT v1 #20478 on…
- PDB
- 1RG1
- 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*T)-3'; Tyrosyl-DNA phosphodiesterase 1
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Ligands
- OTS, SPM, VO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, F | 5'-D(*AP*GP*TP*T)-3' | dna | 3 | — | — |
| A | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 424 | 28% helix, 25% strand | Q9NUW8 |
| B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 429 | 28% 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
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 874 | 0.70 | 0.76 | 87 | empty |
| 2 | 256 | 0.62 | 0.81 | 47 | empty |
| 3 | 101 | 0.35 | 0.74 | 20 | empty |
| 4 | 53 | 0.34 | 0.79 | 15 | OTS |
| 5 | 67 | 0.31 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 600 Ų buried · 5 hydrogen bonds · protein-protein
- F–B · 549 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 541 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1RG1 · 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 1RG1 · PDBe 1RG1 · UniProt Q9NUW8
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