MolNFT v1 · #73960 · protein + RNA
Crystal structure of saccharomyces cerevisiae NEP1/EMG1 bound to S- adenosylhomocysteine and 2 molecules of cognate RNA
3OIJ · Essential for mitotic growth 1: “Crystal structure of saccharomyces cerevisiae NEP1/EMG1 bound to S- adenosylhomocysteine and 2 molecules of…”. X-ray diffraction, 2 ligands (SAH, MG), 8 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 3OIJ
- Type
- protein + RNA
- Length
- 457 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Essential for mitotic growth 1; 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3'
- UniProt
- Q06287
- Ligands
- SAH, MG
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Essential for mitotic growth 1 | protein | 211 | 31% helix, 24% strand | Q06287 |
| B | Essential for mitotic growth 1 | protein | 218 | 28% helix, 23% strand | Q06287 |
| C, D | 5'-R(*GP*GP*GP*CP*UP*UP*CP*AP*AP*CP*GP*CP*CP*C)-3' | rna | 14 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, D, B, C
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.72 | 0.84 | 49 | empty |
| 2 | 333 | 0.65 | 0.80 | 44 | SAH |
| 3 | 267 | 0.63 | 0.81 | 43 | SAH |
| 4 | 99 | 0.56 | 0.86 | 21 | empty |
| 5 | 57 | 0.37 | 0.80 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1485 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 758 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–D · 733 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–D · 416 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 383 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3OIJ · 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 0.98
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 Q06287
- Elsewhere: RCSB PDB 3OIJ · PDBe 3OIJ · UniProt Q06287
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