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Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM2 peptide (region 435-451)
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
- 5LM5
- Type
- protein
- Length
- 656 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Saccharomyces cerevisiae; SYNTHETIC CONSTRUCT
- Molecule
- DNA topoisomerase 2-associated protein PAT1; mRNA decapping protein 2
- UniProt
- P25644, B3LNX5
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.6 · 4 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-associated protein PAT1 | protein | 315 | 73% helix, 3% strand | P25644 |
| B | DNA topoisomerase 2-associated protein PAT1 | protein | 315 | 74% helix, 3% strand | P25644 |
| C | mRNA decapping protein 2 | protein | 14 | 71% helix, 0% strand | B3LNX5 |
| D | mRNA decapping protein 2 | protein | 12 | 67% helix, 0% strand | B3LNX5 |
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 380 | 0.83 | 0.92 | 52 | empty |
| 2 | 323 | 0.82 | 0.92 | 38 | empty |
| 3 | 159 | 0.75 | 0.92 | 31 | empty |
| 4 | 64 | 0.62 | 0.92 | 16 | empty |
| 5 | 76 | 0.58 | 0.88 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2111 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 593 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LM5 · Structure of C-terminal domain from S. cerevisiae PAT1 decapping activator bound to DCP2… · 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
- Every structure of UniProt B3LNX5
- Elsewhere: RCSB PDB 5LM5 · PDBe 5LM5 · UniProt P25644 · UniProt B3LNX5
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