Research workbench
Crystal structure analysis of the yeast tyrosyl-DNA phosphodiesterase H432N_GLU mutant
Analyse Crystal structure analysis of the yeast tyrosyl-DNA phosphodiesterase H432N_GLU… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SQ7
- Type
- protein
- Length
- 1,713 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase 1
- EC
- 3.1.4.-
- UniProt
- P38319
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 432 | 27% helix, 27% strand | P38319 |
| B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 426 | 28% helix, 27% strand | P38319 |
| C | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 430 | 28% helix, 27% strand | P38319 |
| D | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 425 | 28% helix, 27% strand | P38319 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.76 | 0.82 | 86 | SO4 |
| 2 | 318 | 0.76 | 0.87 | 51 | empty |
| 3 | 416 | 0.69 | 0.81 | 40 | empty |
| 4 | 409 | 0.68 | 0.80 | 40 | empty |
| 5 | 839 | 0.68 | 0.74 | 59 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1892 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 643 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 184 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SQ7 · Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N_Glu Mutant · the same entry in another collection · chain D against D, TM-score 1.00
- P38319 · AlphaFold monomer V2.0 prediction for tyrosyl-DNA phosphodiesterase 1 (P38319) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P38319
- Elsewhere: RCSB PDB 3SQ7 · PDBe 3SQ7 · UniProt P38319
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.