MolNFT v1 · #102266 · protein
X-ray structure of the C-terminal domain of PAT1 (decapping activator)
4OGP · DNA topoisomerase 2-associated protein PAT1: “X-ray structure of the C-terminal domain of PAT1 (decapping activator)”. X-ray diffraction, 9 pockets (best druggability 0.81). MolNFT v1 #102266 on GenesisL1: 3D structure, binding…
- PDB
- 4OGP
- Type
- protein
- Length
- 633 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-associated protein PAT1
- UniProt
- P25644
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-associated protein PAT1 | protein | 314 | 72% helix, 3% strand | P25644 |
| B | DNA topoisomerase 2-associated protein PAT1 | protein | 319 | 73% helix, 3% strand | P25644 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.81 | 0.89 | 55 | EDO |
| 2 | 376 | 0.80 | 0.89 | 47 | EDO |
| 3 | 223 | 0.75 | 0.90 | 33 | empty |
| 4 | 117 | 0.69 | 0.90 | 21 | empty |
| 5 | 183 | 0.54 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1850 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4OGP · Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator (Space group… · the same entry in another collection · chain A against A, 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 B 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 P25644
- Elsewhere: RCSB PDB 4OGP · PDBe 4OGP · UniProt P25644
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