Research workbench
Structure of the methyltransferase-like domain of nucleomethylin
Analyse Structure of the methyltransferase-like domain of nucleomethylin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZFU
- Type
- protein
- Length
- 423 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cerebral protein 1
- UniProt
- O43159
- Ligands
- SAH
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cerebral protein 1 | protein | 212 | 40% helix, 21% strand | O43159 |
| B | Cerebral protein 1 | protein | 211 | 39% helix, 22% strand | O43159 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.79 | 0.94 | 36 | SAH |
| 2 | 176 | 0.79 | 0.94 | 35 | SAH |
| 3 | 89 | 0.33 | 0.74 | 23 | empty |
| 4 | 77 | 0.28 | 0.71 | 13 | empty |
| 5 | 53 | 0.26 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 449 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2ZFU · Structure of the methyltransferase-like domain of nucleomethylin · the same entry in another collection · chain A against A, TM-score 1.00
- O43159 · AlphaFold monomer V2.0 prediction for ribosomal RNA-processing protein 8 (O43159) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 O43159
- Elsewhere: RCSB PDB 2ZFU · PDBe 2ZFU · UniProt O43159
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