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Crystal structure of P. abyssi tRNA M1A58 methyltransferase in complex with S-adenosyl-L-homocysteine
Analyse Crystal structure of P. abyssi tRNA M1A58 methyltransferase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LGA
- Type
- protein
- Length
- 1,012 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAM-dependent methyltransferase
- EC
- 2.1.1.36
- UniProt
- Q9V1J7
- Ligands
- SAH, SO4
- Pockets
- 13 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | SAM-dependent methyltransferase (EC 2.1.1.36) | protein | 253 | 28% helix, 34% strand | Q9V1J7 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.76 | 0.98 | 16 | empty |
| 2 | 77 | 0.75 | 0.97 | 16 | empty |
| 3 | 657 | 0.69 | 0.77 | 87 | SAH |
| 4 | 388 | 0.63 | 0.78 | 47 | SO4 |
| 5 | 333 | 0.62 | 0.79 | 39 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2325 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2323 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 805 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 783 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 129 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3LGA · Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with… · the same entry in another collection · chain D against D, 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 B 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 Q9V1J7
- Elsewhere: RCSB PDB 3LGA · PDBe 3LGA · UniProt Q9V1J7
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