MolNFT v1 · #17947 · protein
Crystal structure of RLMA(I) enzyme: 23S rRNA N1-G745 methyltransferase (northeast structural genomics consortium target ER19)
1P91 · Ribosomal RNA large subunit methyltransferase a: “Crystal structure of RLMA(I) enzyme: 23S rRNA N1-G745 methyltransferase (northeast structural genomics…”. X-ray diffraction, 3 ligands (SAM, ZN, SO4), 3 pockets (best druggability…
- PDB
- 1P91
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribosomal RNA large subunit methyltransferase a
- EC
- 2.1.1.51
- UniProt
- P36999
- Ligands
- SAM, ZN, SO4
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribosomal RNA large subunit methyltransferase a (EC 2.1.1.51) | protein | 268 | 27% helix, 30% strand | P36999 |
| B | Ribosomal RNA large subunit methyltransferase a (EC 2.1.1.51) | protein | 258 | 29% helix, 29% strand | P36999 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.80 | 0.81 | 116 | SAM |
| 2 | 110 | 0.39 | 0.75 | 20 | empty |
| 3 | 51 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 863 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 1P91 · Crystal Structure of RlmA(I) enzyme: 23S rRNA n1-G745 methyltransferase (NORTHEAST… · the same entry in another collection · chain B against B, TM-score 1.00
- P36999 · AlphaFold monomer V2.0 prediction for 23S rRNA (GUANINE(745)-N(1))-methyltransferase… · a predicted model of the same protein · chain B 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 P36999
- Elsewhere: RCSB PDB 1P91 · PDBe 1P91 · UniProt P36999
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.