Research workbench
Crystal structure of human N6amt1-Trm112 in complex with SAM (space group P6122)
Analyse Crystal structure of human N6amt1-Trm112 in complex with SAM (space group P6122) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KMR
- Type
- protein
- Length
- 321 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- Multifunctional methyltransferase subunit TRM112-like protein; Methyltransferase N6AMT1
- EC
- 2.1.1.-, 2.1.1.72
- UniProt
- Q9UI30, Q9Y5N5
- Ligands
- SAM
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Multifunctional methyltransferase subunit TRM112-like protein | protein | 125 | 32% helix, 22% strand | Q9UI30 |
| B | Methyltransferase N6AMT1 (EC 2.1.1.-, 2.1.1.72) | protein | 196 | 39% helix, 29% strand | Q9Y5N5 |
Ligands and binding sites
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 | 258 | 0.70 | 0.85 | 54 | SAM |
| 2 | 116 | 0.63 | 0.87 | 22 | empty |
| 3 | 116 | 0.41 | 0.76 | 18 | empty |
| 4 | 56 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1242 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6KMR · Crystal structure of human N6AMT1-TRM112 in complex with SAM (space group P6122) · 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 B against A, TM-score 0.99
- Q9UI30 · AlphaFold monomer V2.0 prediction for multifunctional methyltransferase subunit… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9UI30
- Every structure of UniProt Q9Y5N5
- Elsewhere: RCSB PDB 6KMR · PDBe 6KMR · UniProt Q9UI30 · UniProt Q9Y5N5
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