MolNFT v1 · #138898 · protein
Crystal structure of the methyltranferase domain of human HEN1 in complex with adomet
5WY0 · Small RNA 2'-O-methyltransferase: “Crystal structure of the methyltranferase domain of human HEN1 in complex with adomet”. X-ray diffraction, 1 ligand (SAM), 2 pockets (best druggability 0.46). MolNFT v1 #138898 on GenesisL1: 3D…
- PDB
- 5WY0
- Type
- protein
- Length
- 199 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small RNA 2'-O-methyltransferase
- EC
- 2.1.1.-
- UniProt
- Q5T8I9
- Ligands
- SAM
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small RNA 2'-O-methyltransferase (EC 2.1.1.-) | protein | 199 | 33% helix, 27% strand | Q5T8I9 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.46 | 0.76 | 25 | SAM |
| 2 | 192 | 0.46 | 0.74 | 19 | empty |
Compared structures
- 5WY0 · Crystal structure of the methyltranferase domain of human HEN1 in complex with AdoMet · the same entry in another collection · chain A against A, TM-score 1.00
- Q5T8I9 · AlphaFold monomer V2.0 prediction for small RNA 2'-O-methyltransferase (Q5T8I9) · 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 Q5T8I9
- Elsewhere: RCSB PDB 5WY0 · PDBe 5WY0 · UniProt Q5T8I9
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