MolNFT v1 · #17680 · protein
Crystal structure of the set domain of lsmt bound to melysine and adohcy
1P0Y · Ribulose-1,5 bisphosphate CARBOXYLASE/OXYGENASE large…: “Crystal structure of the set domain of lsmt bound to melysine and adohcy”. X-ray diffraction, 2 ligands (SAH, MLZ), 14 pockets (best druggability 0.81). MolNFT v1 #17680 on…
- 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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