Research workbench
Structure of PPM1, a leucine carboxy methyltransferase involved in the regulation of protein phosphatase 2A activity
Analyse Structure of PPM1, a leucine carboxy methyltransferase involved in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RJD
- Type
- protein
- Length
- 990 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxy methyl transferase for protein phosphatase 2A catalytic subunit
- EC
- 2.1.1.-
- UniProt
- Q04081
- Ligands
- SAM, SO4
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxy methyl transferase for protein phosphatase 2A catalytic subunit (EC 2.1.1.-) | protein | 328 | 53% helix, 15% strand | Q04081 |
| B | Carboxy methyl transferase for protein phosphatase 2A catalytic subunit (EC 2.1.1.-) | protein | 329 | 53% helix, 16% strand | Q04081 |
| C | Carboxy methyl transferase for protein phosphatase 2A catalytic subunit (EC 2.1.1.-) | protein | 333 | 53% helix, 16% strand | Q04081 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · chains C
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.80 | 0.84 | 68 | empty |
| 2 | 543 | 0.77 | 0.84 | 63 | SAM, BME |
| 3 | 512 | 0.76 | 0.84 | 58 | SAM, BME |
| 4 | 471 | 0.75 | 0.83 | 57 | SAM, BME |
| 5 | 262 | 0.73 | 0.87 | 52 | empty |
Interfaces
2 interfaces between chains.
- A–C · 964 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 659 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (additive adduct).
Compared structures
- 1RJD · Structure of PPM1, a leucine carboxy methyltransferase involved in the regulation of… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04081 · AlphaFold monomer V2.0 prediction for leucine carboxyl methyltransferase 1 (Q04081) · 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 Q04081
- Elsewhere: RCSB PDB 1RJD · PDBe 1RJD · UniProt Q04081
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