Research workbench
Crystal structure analysis of the yeast tyrosyl-DNA phosphodiesterase H432N mutant
Analyse Crystal structure analysis of the yeast tyrosyl-DNA phosphodiesterase H432N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SQ5
- Type
- protein
- Length
- 1,679 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
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 419 | 27% helix, 28% strand | P38319 |
| B | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 420 | 28% helix, 28% strand | P38319 |
| C | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 422 | 27% helix, 28% strand | P38319 |
| D | Tyrosyl-DNA phosphodiesterase 1 (EC 3.1.4.-) | protein | 418 | 28% helix, 28% strand | P38319 |
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.80 | 0.82 | 99 | empty |
| 2 | 954 | 0.77 | 0.80 | 65 | empty |
| 3 | 369 | 0.62 | 0.78 | 31 | empty |
| 4 | 180 | 0.45 | 0.75 | 30 | empty |
| 5 | 99 | 0.45 | 0.80 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 847 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 289 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 234 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 73 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3SQ5 · Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N 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 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 P38319
- Elsewhere: RCSB PDB 3SQ5 · PDBe 3SQ5 · UniProt P38319
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