Research workbench
Crystal structure of the set domain of lsmt bound to melysine and adohcy
Analyse Crystal structure of the set domain of lsmt bound to melysine and adohcy in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P0Y
- Type
- protein
- Length
- 1,310 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase…
- EC
- 2.1.1.127
- UniProt
- Q43088
- Ligands
- SAH, MLZ
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase, chloroplast (EC 2.1.1.127) | protein | 430 | 45% helix, 10% strand | Q43088 |
| B | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase, chloroplast (EC 2.1.1.127) | protein | 441 | 49% helix, 12% strand | Q43088 |
| C | Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase, chloroplast (EC 2.1.1.127) | protein | 439 | 46% helix, 13% strand | Q43088 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- MLZ · N-methyl-lysine · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.81 | 0.83 | 74 | empty |
| 2 | 496 | 0.71 | 0.81 | 54 | SAH, MLZ |
| 3 | 540 | 0.71 | 0.80 | 48 | SAH, MLZ |
| 4 | 317 | 0.63 | 0.80 | 35 | MLZ |
| 5 | 217 | 0.57 | 0.79 | 24 | SAH |
Interfaces
3 interfaces between chains.
- A–B · 1466 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1439 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1419 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1P0Y · Crystal structure of the SET domain of LSMT bound to MeLysine and AdoHcy · the same entry in another collection · chain A against A, TM-score 1.00
- Q43088 · AlphaFold monomer V2.0 prediction for ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE… · a predicted model of the same protein · chain C 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 Q43088
- Elsewhere: RCSB PDB 1P0Y · PDBe 1P0Y · UniProt Q43088
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