Research workbench
Structure of C-terminal domain from S. cerevisiae PAT1 decapping activator bound to DCP2 HLM10 peptide (region 954-970)
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
- 5LMG
- Type
- protein
- Length
- 663 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
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-associated protein PAT1 | protein | 316 | 72% helix, 3% strand | P25644 |
| B | DNA topoisomerase 2-associated protein PAT1 | protein | 321 | 74% helix, 3% strand | P25644 |
| C | MRNA decapping protein 2 | protein | 13 | 77% helix, 0% strand | B3LNX5 |
| D | MRNA decapping protein 2 | protein | 13 | 69% helix, 0% strand | B3LNX5 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.84 | 0.92 | 62 | EDO, TRS |
| 2 | 239 | 0.78 | 0.91 | 35 | EDO |
| 3 | 55 | 0.64 | 0.94 | 18 | EDO |
| 4 | 55 | 0.61 | 0.92 | 20 | empty |
| 5 | 157 | 0.50 | 0.78 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2182 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 595 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 585 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5LMG · 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 5LMG · PDBe 5LMG · UniProt P25644 · UniProt B3LNX5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.