MolNFT v1 · #153633 · protein
Crystal structure and catalytic mechanism of the essential M1G37 tRNA methyltransferase trmd from pseudomonas aeruginosa
6JKI · TRNA (guanine-N(1)-)-methyltransferase: “Crystal structure and catalytic mechanism of the essential M1G37 tRNA methyltransferase trmd from pseudomonas…”. X-ray diffraction, 3 ligands (SFG, MN, NA), 4 pockets (best druggability…
- PDB
- 6JKI
- Type
- protein
- Length
- 485 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, MN, NA
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 241 | 42% helix, 18% strand | Q02RL6 |
| B | TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228) | protein | 244 | 42% helix, 18% strand | Q02RL6 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- GOL · Glycerol · additive · 10 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.74 | 0.87 | 43 | SFG, GOL |
| 2 | 265 | 0.72 | 0.86 | 43 | SFG, MN |
| 3 | 170 | 0.48 | 0.77 | 23 | GOL, NA |
| 4 | 135 | 0.43 | 0.76 | 20 | PEG |
Interfaces
1 interface between chains.
- A–B · 3802 Ų buried · 76 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6JKI · 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 6JKI · PDBe 6JKI · UniProt Q02RL6
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