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Crystal structure of Mmi1 YTH domain
Analyse Crystal structure of Mmi1 YTH domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DNP
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- Schizosaccharomyces pombe 972h-
- Molecule
- YTH domain-containing protein mmi1
- UniProt
- O74958
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YTH domain-containing protein mmi1 | protein | 145 | 32% helix, 34% strand | O74958 |
| B | YTH domain-containing protein mmi1 | protein | 134 | 35% helix, 34% strand | O74958 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.56 | 0.74 | 34 | PO4 |
| 2 | 63 | 0.37 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 O74958
- Elsewhere: RCSB PDB 5DNP · PDBe 5DNP · UniProt O74958
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