MolNFT v1 · #73964 · protein + RNA
Crystal structure of saccharomyces cerevisiae NEP1/EMG1 bound to S- adenosylhomocysteine and 1 molecule of cognate RNA
3OIN · Ribosomal RNA small subunit methyltransferase NEP1: “Crystal structure of saccharomyces cerevisiae NEP1/EMG1 bound to S- adenosylhomocysteine and 1 molecule of…”. X-ray diffraction, 3 ligands (SAH, MG, CL), 4 pockets (best…
- PDB
- 3OIN
- Type
- protein + RNA
- Length
- 448 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA small subunit methyltransferase NEP1…
- EC
- 2.1.1.260
- UniProt
- Q06287
- Ligands
- SAH, MG, CL
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribosomal RNA small subunit methyltransferase NEP1 (EC 2.1.1.260) | protein | 217 | 29% helix, 24% strand | Q06287 |
| C | 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 · chains B, C
- MG · Magnesium ion · metal · chains C
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.76 | 0.81 | 86 | empty |
| 2 | 276 | 0.64 | 0.81 | 42 | SAH |
| 3 | 88 | 0.43 | 0.79 | 21 | empty |
| 4 | 82 | 0.36 | 0.76 | 16 | CL |
Interfaces
3 interfaces between chains.
- A–B · 1504 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 729 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–C · 434 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (acetylation).
Compared structures
- 3OIN · 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 3OIN · PDBe 3OIN · UniProt Q06287
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