MolNFT v1 · #72302 · protein
Putative RNA methyltransferase from yersinia pestis in complex with S- adenosyl-L-homocysteine.
3N4K: “Putative RNA methyltransferase from yersinia pestis in complex with S- adenosyl-L-homocysteine.”. X-ray diffraction, 1 ligand (SAH), 4 pockets (best druggability 0.66). MolNFT v1 #72302 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3N4K
- Type
- protein
- Length
- 324 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA methyltransferase
- UniProt
- Q74Y93
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA methyltransferase | protein | 163 | 36% helix, 15% strand | Q74Y93 |
| B | RNA methyltransferase | protein | 161 | 35% helix, 18% strand | Q74Y93 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 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 | 338 | 0.66 | 0.80 | 46 | SAH |
| 2 | 220 | 0.60 | 0.81 | 29 | empty |
| 3 | 104 | 0.42 | 0.77 | 20 | empty |
| 4 | 74 | 0.37 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1538 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 3N4K · Putative RNA methyltransferase from Yersinia pestis in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q74Y93 · AlphaFold monomer V2.0 prediction for tRNA (CYTIDINE(34)-2'-O)-methyltransferase (Q74Y93) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q74Y93
- Elsewhere: RCSB PDB 3N4K · PDBe 3N4K · UniProt Q74Y93
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