Research workbench
Crystal structure of adomet bound rRNA methyltransferase from sinorhizobium meliloti
Analyse Crystal structure of adomet bound rRNA methyltransferase from sinorhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L0Z
- Type
- protein
- Length
- 523 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable RNA methyltransferase, trmh family
- EC
- 2.1.1.-
- UniProt
- Q92SJ4
- Ligands
- SAM, CO, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable RNA methyltransferase, trmh family (EC 2.1.1.-) | protein | 262 | 38% helix, 22% strand | Q92SJ4 |
| B | Probable RNA methyltransferase, trmh family (EC 2.1.1.-) | protein | 261 | 38% helix, 21% strand | Q92SJ4 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.74 | 0.81 | 66 | SO4, SAM |
| 2 | 147 | 0.44 | 0.76 | 26 | empty |
| 3 | 76 | 0.41 | 0.79 | 18 | empty |
| 4 | 58 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1381 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5L0Z · Crystal Structure of AdoMet bound rRNA methyltransferase from Sinorhizobium meliloti · the same entry in another collection · chain A against A, TM-score 1.00
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 Q92SJ4
- Elsewhere: RCSB PDB 5L0Z · PDBe 5L0Z · UniProt Q92SJ4
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