MolNFT v1 · #35624 · protein
Crystal structure of rRNA methyltransferase with SAM ligand
2EGV · UPF0088 protein AQ_165: “Crystal structure of rRNA methyltransferase with SAM ligand”. X-ray diffraction, 1 ligand (SAM), 6 pockets (best druggability 0.65). MolNFT v1 #35624 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2EGV
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0088 protein AQ_165
- UniProt
- O66552
- Ligands
- SAM
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | UPF0088 protein AQ_165 | protein | 229 | 31% helix, 29% strand | O66552 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.65 | 0.84 | 35 | SAM |
| 2 | 335 | 0.65 | 0.80 | 43 | SAM |
| 3 | 81 | 0.34 | 0.75 | 15 | empty |
| 4 | 76 | 0.31 | 0.73 | 10 | empty |
| 5 | 61 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1510 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2EGV · Crystal structure of rRNA methyltransferase with SAM ligand · the same entry in another collection · chain A against A, TM-score 1.00
- O66552 · AlphaFold monomer V2.0 prediction for ribosomal RNA small subunit methyltransferase E… · 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 O66552
- Elsewhere: RCSB PDB 2EGV · PDBe 2EGV · UniProt O66552
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