Research workbench
Crystal structure of MARF1 nyn domain from mus musculus
Analyse Crystal structure of MARF1 nyn domain from mus musculus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YAA
- Type
- protein
- Length
- 598 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Meiosis regulator and mRNA stability factor 1
- UniProt
- Q8BJ34
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Meiosis regulator and mRNA stability factor 1 | protein | 150 | 41% helix, 23% strand | Q8BJ34 |
| C | Meiosis regulator and mRNA stability factor 1 | protein | 149 | 40% helix, 23% strand | Q8BJ34 |
| D | Meiosis regulator and mRNA stability factor 1 | protein | 149 | 41% helix, 23% strand | Q8BJ34 |
Ligands and binding sites
- GOL · Glycerol · additive · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.75 | 0.80 | 74 | empty |
| 2 | 76 | 0.43 | 0.81 | 18 | GOL |
| 3 | 63 | 0.39 | 0.80 | 14 | empty |
| 4 | 51 | 0.31 | 0.77 | 17 | empty |
Interfaces
4 interfaces between chains.
- C–D · 463 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 150 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 147 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 144 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 5YAA · Crystal structure of Marf1 NYN domain from Mus musculus · the same entry in another collection · chain A against A, TM-score 1.00
- Q8BJ34 · AlphaFold monomer V2.0 prediction for meiosis regulator and mRNA stability factor 1… · a predicted model of the same protein · chain C 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 Q8BJ34
- Elsewhere: RCSB PDB 5YAA · PDBe 5YAA · UniProt Q8BJ34
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