MolNFT v1 · #71330 · protein
Crystal structure of P. abyssi tRNA M1A58 methyltransferase in complex with S-adenosyl-L-methionine
3MB5 · SAM-dependent methyltransferase: “Crystal structure of P. abyssi tRNA M1A58 methyltransferase in complex with S-adenosyl-L-methionine”. X-ray diffraction, 2 ligands (SAM, SO4), 1 pocket (best druggability 0.51). MolNFT v1 #71330 on…
- PDB
- 3MB5
- Type
- protein
- Length
- 255 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferase
- EC
- 2.1.1.36
- UniProt
- Q9V1J7
- Ligands
- SAM, SO4
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SAM-dependent methyltransferase (EC 2.1.1.36) | protein | 255 | 29% helix, 30% strand | Q9V1J7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.51 | 0.79 | 30 | SAM |
Compared structures
- 3MB5 · Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9V1J7 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(57)-N(1)/ADENINE(58)-N(1))-methyltrans… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9V1J7
- Elsewhere: RCSB PDB 3MB5 · PDBe 3MB5 · UniProt Q9V1J7
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