Research workbench
Structure of C-terminal domain from S. cerevisiae PAT1 decapping activator (space group : P212121)
Analyse Structure of C-terminal domain from S. cerevisiae PAT1 decapping activator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OJJ
- Type
- protein
- Length
- 915 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-associated protein PAT1
- UniProt
- P25644
- Ligands
- MG, CL
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA topoisomerase 2-associated protein PAT1 | protein | 323 | 73% helix, 3% strand | P25644 |
| A | DNA topoisomerase 2-associated protein PAT1 | protein | 314 | 73% helix, 1% strand | P25644 |
| B | DNA topoisomerase 2-associated protein PAT1 | protein | 278 | 74% helix, 4% strand | P25644 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · chains C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.75 | 0.79 | 76 | empty |
| 2 | 525 | 0.73 | 0.81 | 43 | empty |
| 3 | 190 | 0.67 | 0.86 | 24 | empty |
| 4 | 230 | 0.64 | 0.82 | 32 | empty |
| 5 | 203 | 0.57 | 0.80 | 25 | empty |
Interfaces
2 interfaces between chains.
- C–A · 868 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 253 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OJJ · Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator (Space group… · the same entry in another collection · chain C against C, TM-score 1.00
- P25644 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-associated protein PAT1 (P25644) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P25644
- Elsewhere: RCSB PDB 4OJJ · PDBe 4OJJ · UniProt P25644
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