MolNFT v1 · #73959 · protein
Crystal structure of saccharomyces cerevisiae NEP1/EMG1 bound to S- adenosylhomocysteine
3OII · Essential for mitotic growth 1: “Crystal structure of saccharomyces cerevisiae NEP1/EMG1 bound to S- adenosylhomocysteine”. X-ray diffraction, 1 ligand (SAH), 4 pockets (best druggability 0.63). MolNFT v1 #73959 on GenesisL1: 3D…
- PDB
- 3OII
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Essential for mitotic growth 1
- UniProt
- Q06287
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Essential for mitotic growth 1 | protein | 216 | 29% helix, 25% strand | Q06287 |
| B | Essential for mitotic growth 1 | protein | 208 | 30% helix, 22% strand | Q06287 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.63 | 0.81 | 45 | SAH |
| 2 | 164 | 0.60 | 0.83 | 35 | empty |
| 3 | 235 | 0.59 | 0.80 | 32 | SAH |
| 4 | 77 | 0.40 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1569 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3OII · Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine · the same entry in another collection · chain A against A, TM-score 1.00
- Q06287 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase NEP1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q06287
- Elsewhere: RCSB PDB 3OII · PDBe 3OII · UniProt Q06287
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