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Structure of C-terminal domain from S. cerevisiae PAT1 decapping activator bound to DCP2 HLM3 peptide (region 484-500)
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
- 5LMF
- Type
- protein
- Length
- 664 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-associated protein PAT1; MRNA decapping protein 2
- UniProt
- P25644, B3LNX5
- Ligands
- MG, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-associated protein PAT1 | protein | 312 | 71% helix, 3% strand | P25644 |
| B | DNA topoisomerase 2-associated protein PAT1 | protein | 318 | 72% helix, 3% strand | P25644 |
| C, D | MRNA decapping protein 2 | protein | 17 | 71% helix, 0% strand | B3LNX5 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.83 | 0.92 | 65 | EDO |
| 2 | 195 | 0.76 | 0.91 | 36 | empty |
| 3 | 64 | 0.65 | 0.93 | 20 | empty |
| 4 | 62 | 0.62 | 0.92 | 18 | empty |
| 5 | 165 | 0.58 | 0.82 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2035 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 667 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 619 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5LMF · 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 A 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 5LMF · PDBe 5LMF · UniProt P25644 · UniProt B3LNX5
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