MolNFT v1 · #138920 · protein
Crystal structure and catalytic mechanism of the essential M1G37 tRNA methyltransferase trmd from pseudomonas aeruginosa
5WYR · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure and catalytic mechanism of the essential M1G37 tRNA methyltransferase trmd from pseudomonas…”. X-ray diffraction, 1 ligand (SFG), 4 pockets (best druggability 0.80). MolNFT…
- PDB
- 5WYR
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (guanine-N(1)-)-methyltransferase
- EC
- 2.1.1.228
- UniProt
- Q02RL6
- Ligands
- SFG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 242 | 42% helix, 19% strand | Q02RL6 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 248 | 42% helix, 18% strand | Q02RL6 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.80 | 0.98 | 35 | SFG |
| 2 | 557 | 0.74 | 0.82 | 63 | SFG |
| 3 | 193 | 0.54 | 0.79 | 32 | empty |
| 4 | 82 | 0.40 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3961 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 5WYR · Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q02RL6 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (Q02RL6) · 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 Q02RL6
- Elsewhere: RCSB PDB 5WYR · PDBe 5WYR · UniProt Q02RL6
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