MolNFT v1 · #111431 · protein
Crystal structure of trmd, a M1G37 tRNA methyltransferase with SAM- competitive compounds
4YQO · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure of trmd, a M1G37 tRNA methyltransferase with SAM- competitive compounds”. X-ray diffraction, 1 ligand (4H1), 1 pocket (best druggability 0.51). MolNFT v1 #111431 on…
- PDB
- 4YQO
- Type
- protein
- Length
- 242 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- P43912
- Ligands
- 4H1
- Pockets
- 1 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 242 | 43% helix, 17% strand | P43912 |
Ligands and binding sites
- 4H1 · 6-({[(1R,3S)-3-(aminomethyl)cyclohexyl]methyl}amino)pyridine-3-carboxamide · ligand · 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 | 96 | 0.51 | 0.83 | 25 | 4H1 |
Compared structures
- 4YQO · Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds · the same entry in another collection · chain A against A, TM-score 1.00
- P43912 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (P43912) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P43912
- Elsewhere: RCSB PDB 4YQO · PDBe 4YQO · UniProt P43912
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