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Structure and catalytic mechanism of a set domain protein methyltransferase
Analyse Structure and catalytic mechanism of a set domain protein methyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MLV
- Type
- protein
- Length
- 1,302 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribulose-1,5 biphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase
- EC
- 2.1.1.127
- UniProt
- Q43088
- Ligands
- SAH
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribulose-1,5 biphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 424 | 46% helix, 11% strand | Q43088 |
| B | Ribulose-1,5 biphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 440 | 49% helix, 12% strand | Q43088 |
| C | Ribulose-1,5 biphosphate CARBOXYLASE/OXYGENASE large subunit N-methyltransferase (EC 2.1.1.127) | protein | 438 | 46% helix, 12% strand | Q43088 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, B, C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1070 | 0.82 | 0.83 | 111 | empty |
| 2 | 643 | 0.76 | 0.82 | 69 | SAH, EPE |
| 3 | 710 | 0.76 | 0.81 | 82 | SAH, EPE |
| 4 | 635 | 0.75 | 0.81 | 65 | SAH, EPE |
| 5 | 63 | 0.41 | 0.80 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1434 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1429 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1392 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1MLV · Structure and Catalytic Mechanism of a SET Domain Protein Methyltransferase · 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 1MLV · PDBe 1MLV · UniProt Q43088
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