Research workbench
Human putative TRNA(1-METHYLADENOSINE)METHYLTRANSFERASE
Analyse Human putative TRNA(1-METHYLADENOSINE)METHYLTRANSFERASE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B25
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q9BVS5
- Ligands
- SAM, UNX
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 254 | 28% helix, 29% strand | Q9BVS5 |
| B | Hypothetical protein | protein | 239 | 29% helix, 29% strand | Q9BVS5 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.57 | 0.79 | 39 | SAM, UNX |
| 2 | 189 | 0.54 | 0.79 | 36 | SAM, UNX |
| 3 | 76 | 0.35 | 0.76 | 19 | empty |
| 4 | 69 | 0.33 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 174 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2B25 · Human putative tRNA(1-methyladenosine)methyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BVS5 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase… · a predicted model of the same protein · chain A 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 Q9BVS5
- Elsewhere: RCSB PDB 2B25 · PDBe 2B25 · UniProt Q9BVS5
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