MolNFT v1 · #172289 · protein
Structure of archaeoglobus fulgidus TRM11-TRM112 M2G10 tRNA methyltransferase complex bound to sinefungin
6ZXW · TRNA (GUANINE(10)-N2)-dimethyltransferase: “Structure of archaeoglobus fulgidus TRM11-TRM112 M2G10 tRNA methyltransferase complex bound to sinefungin”. X-ray diffraction, 3 ligands (SFG, ZN, SO4), 4 pockets (best druggability 0.62).…
- PDB
- 6ZXW
- Type
- protein
- Length
- 378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (GUANINE(10)-N2)-dimethyltransferase; Uncharacterized protein
- UniProt
- A0A117KU88, A0A117KMN5
- Ligands
- SFG, ZN, SO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | TRNA (GUANINE(10)-N2)-dimethyltransferase | protein | 321 | 30% helix, 35% strand | A0A117KU88 |
| H | Uncharacterized protein | protein | 57 | 9% helix, 47% strand | A0A117KMN5 |
Ligands and binding sites
- SFG · Sinefungin · ligand · chains G
- ZN · Zinc ion · metal · chains H
- SO4 · Sulfate ion · ion · 2 copies · chains G
- EDO · 1,2-ethanediol · additive · 10 copies · chains G, H
- ACY · Acetic acid · additive · 2 copies · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 287 | 0.62 | 0.80 | 33 | SFG, EDO |
| 2 | 61 | 0.50 | 0.86 | 16 | EDO |
| 3 | 87 | 0.38 | 0.77 | 12 | empty |
| 4 | 82 | 0.32 | 0.73 | 17 | EDO, ACY |
Interfaces
1 interface between chains.
- G–H · 952 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6ZXW · Structure of Archaeoglobus fulgidus Trm11-Trm112 m2G10 tRNA methyltransferase complex… · the same entry in another collection · chain G against G, 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
- Every structure of UniProt A0A117KMN5
- Elsewhere: RCSB PDB 6ZXW · PDBe 6ZXW · UniProt A0A117KU88 · UniProt A0A117KMN5
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