Research workbench
Crystal structure of C21ORF127-TRMT112 in complex with sah and H4 peptide
Analyse Crystal structure of C21ORF127-TRMT112 in complex with sah and H4 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H1E
- Type
- protein
- Length
- 327 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 3 distinct chains · 36% 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 |
| S | Histone H4 peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, S
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 | 190 | 0.78 | 0.93 | 43 | SAH |
| 2 | 96 | 0.58 | 0.86 | 21 | empty |
| 3 | 211 | 0.51 | 0.76 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1214 Ų buried · 12 hydrogen bonds · protein-protein
- A–S · 317 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 6H1E · Crystal structure of C21orf127-TRMT112 in complex with SAH and H4 peptide · 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 0.98
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 6H1E · PDBe 6H1E · UniProt Q9Y5N5 · UniProt Q9UI30
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