Research workbench
Crystal structure of HEMK2-TRMT112 complex
Analyse Crystal structure of HEMK2-TRMT112 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PED
- Type
- protein
- Length
- 319 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase N6AMT1; Multifunctional methyltransferase subunit TRM112-like protein
- EC
- 2.1.1.-, 2.1.1.72
- UniProt
- Q9Y5N5, Q9UI30
- Ligands
- SAH, UNX
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase N6AMT1 (EC 2.1.1.-, 2.1.1.72) | protein | 193 | 38% helix, 28% strand | Q9Y5N5 |
| B | Multifunctional methyltransferase subunit TRM112-like protein | protein | 126 | 32% helix, 22% strand | Q9UI30 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- UNX · Unknown atom or ion · ion · 12 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 | 215 | 0.77 | 0.91 | 43 | SAH, UNX |
| 2 | 89 | 0.55 | 0.85 | 21 | UNX |
| 3 | 55 | 0.34 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6PED · Crystal structure of HEMK2-TRMT112 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5N5 · AlphaFold monomer V2.0 prediction for methyltransferase N6AMT1 (Q9Y5N5) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9UI30 · AlphaFold monomer V2.0 prediction for multifunctional methyltransferase subunit… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q9Y5N5
- Every structure of UniProt Q9UI30
- Elsewhere: RCSB PDB 6PED · PDBe 6PED · UniProt Q9Y5N5 · UniProt Q9UI30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.