Research workbench
Crystal structure of a SAM-dependent methyltransferase lepi in complex with its substrate
Analyse Crystal structure of a SAM-dependent methyltransferase lepi in complex with its… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J24
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-methyltransferase
- UniProt
- A0A364MK46
- Ligands
- BYO, SAM
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | O-methyltransferase | protein | 387 | 53% helix, 13% strand | A0A364MK46 |
Ligands and binding sites
- BYO · (3~{S},4'~{R},4'~{A}~{S},6'~{R},8'~{A}~{S})-4',6'-dimethyl-5-phenyl-spiro[1~{h}-pyridine-3,5'-2,3,4, 4~{A},6,8~{A}-hexahydro-1~{H}-naphthalene]-2,4-dione · ligand · 2 copies · chains B, A
- SAM · S-adenosylmethionine · ligand · 2 copies · chains B, A
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 | 1153 | 0.86 | 0.87 | 90 | BYO, SAM |
| 2 | 1186 | 0.86 | 0.86 | 94 | BYO, SAM |
| 3 | 200 | 0.56 | 0.79 | 23 | empty |
| 4 | 178 | 0.52 | 0.78 | 23 | empty |
| 5 | 110 | 0.48 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- B–A · 5125 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6J24 · Crystal structure of a SAM-dependent methyltransferase LepI in complex with its substrate · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A364MK46
- Elsewhere: RCSB PDB 6J24 · PDBe 6J24 · UniProt A0A364MK46
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