MolNFT v1 · #20458 · protein + DNA
Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octapeptide klnyydpr, and tetranucleotide agtt.
1RFF · 5'-D(*AP*GP*TP*T)-3': “Crystal structure of human tyrosyl-DNA phosphodiesterase complexed with vanadate, octapeptide klnyydpr, and…”. X-ray diffraction, 2 ligands (SPM, VO4), 4 pockets (best druggability 0.74). MolNFT v1 #20458 on…
- PDB
- 1RFF
- Type
- protein + DNA
- Length
- 872 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*GP*TP*T)-3'; Tyrosyl-DNA phosphodiesterase 1; Topoisomerase I-derived peptide
- EC
- 3.1.4.-
- UniProt
- Q9NUW8
- Ligands
- SPM, VO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 24% 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 | 425 | 28% helix, 25% strand | Q9NUW8 |
| B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 429 | 27% helix, 24% strand | Q9NUW8 |
| C, E | Topoisomerase I-derived peptide | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- SPM · Spermine · ligand · 2 copies · chains A, C, B, E
- VO4 · Vanadate ion · ion · 2 copies · chains D, A, C, F, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.74 | 0.77 | 115 | empty |
| 2 | 153 | 0.45 | 0.76 | 25 | empty |
| 3 | 121 | 0.44 | 0.78 | 17 | empty |
| 4 | 69 | 0.36 | 0.77 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–B · 589 Ų buried · 4 hydrogen bonds · protein-protein
- F–B · 559 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–A · 547 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 430 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 427 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1RFF · Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate… · the same entry in another collection · chain E against E, 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 1RFF · PDBe 1RFF · UniProt Q9NUW8
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