Research workbench
Crystal structure analysis of the yeast tyrosyl-DNA phosphodiesterase
Analyse Crystal structure analysis of the yeast tyrosyl-DNA phosphodiesterase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q32
- Type
- protein
- Length
- 1,671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosyl-DNA phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- P38319
- Pockets
- 11 · 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 (EC 3.1.4.-) | protein | 419 | 28% helix, 28% strand | P38319 |
| B | Tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) | protein | 420 | 27% helix, 27% strand | P38319 |
| C | Tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) | protein | 417 | 27% helix, 28% strand | P38319 |
| D | Tyrosyl-DNA phosphodiesterase (EC 3.1.4.-) | protein | 415 | 29% helix, 27% strand | P38319 |
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.80 | 0.82 | 121 | empty |
| 2 | 188 | 0.48 | 0.76 | 29 | empty |
| 3 | 149 | 0.44 | 0.76 | 26 | empty |
| 4 | 113 | 0.42 | 0.77 | 21 | empty |
| 5 | 86 | 0.40 | 0.77 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 896 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 52 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Q32 · Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase · 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 B 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 1Q32 · PDBe 1Q32 · UniProt P38319
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