Research workbench
Crystal structure and catalytic mechanism of the essential M1G37 tRNA methyltransferase trmd from pseudomonas aeruginosa
Analyse Crystal structure and catalytic mechanism of the essential M1G37 tRNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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