Research workbench
Crystal structure of C21orf127-TRMT112 in complex with SAH
Analyse Crystal structure of C21orf127-TRMT112 in complex with SAH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H1D
- Type
- protein
- Length
- 322 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.94
- Source
- Homo sapiens
- Molecule
- HemK methyltransferase family member 2; Multifunctional methyltransferase subunit…
- EC
- 2.1.1.-
- UniProt
- Q9Y5N5, Q9UI30
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.94 · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HemK methyltransferase family member 2 (EC 2.1.1.-) | protein | 207 | 38% helix, 26% strand | Q9Y5N5 |
| B | Multifunctional methyltransferase subunit TRM112-like protein | protein | 115 | 35% helix, 23% strand | Q9UI30 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.78 | 0.93 | 42 | SAH |
| 2 | 97 | 0.59 | 0.86 | 22 | empty |
| 3 | 195 | 0.51 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1210 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6H1D · Crystal structure of C21ORF127-TRMT112 in complex with sah · 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 0.97
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 6H1D · PDBe 6H1D · UniProt Q9Y5N5 · UniProt Q9UI30
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