MolNFT v1 · #172288 · protein
Structure of archaeoglobus fulgidus TRM11 M2G10 tRNA methyltransferase enzyme bound to sinefungin
6ZXV · TRNA (GUANINE(10)-N2)-dimethyltransferase: “Structure of archaeoglobus fulgidus TRM11 M2G10 tRNA methyltransferase enzyme bound to sinefungin”. X-ray diffraction, 1 ligand (SFG), 3 pockets (best druggability 0.60). MolNFT v1 #172288…
- PDB
- 6ZXV
- Type
- protein
- Length
- 648 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (GUANINE(10)-N2)-dimethyltransferase
- UniProt
- A0A117KU88
- Ligands
- SFG
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (GUANINE(10)-N2)-dimethyltransferase | protein | 325 | 30% helix, 35% strand | A0A117KU88 |
| B | TRNA (GUANINE(10)-N2)-dimethyltransferase | protein | 323 | 32% helix, 36% strand | A0A117KU88 |
Ligands and binding sites
- SFG · Sinefungin · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.60 | 0.80 | 37 | SFG |
| 2 | 273 | 0.60 | 0.79 | 30 | SFG |
| 3 | 104 | 0.37 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 62 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6ZXV · Structure of Archaeoglobus fulgidus Trm11 m2G10 tRNA methyltransferase enzyme bound to… · the same entry in another collection · chain B against B, TM-score 1.00
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 A0A117KU88
- Elsewhere: RCSB PDB 6ZXV · PDBe 6ZXV · UniProt A0A117KU88
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