MolNFT v1 · #125118 · protein
Crystal structure of rRNA methyltransferase from sinorhizobium meliloti
5KZK · Probable RNA methyltransferase, trmh family: “Crystal structure of rRNA methyltransferase from sinorhizobium meliloti”. X-ray diffraction, 2 ligands (CO, SO4), 2 pockets (best druggability 0.68). MolNFT v1 #125118 on GenesisL1: 3D…
- PDB
- 5KZK
- Type
- protein
- Length
- 521 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
- CO, SO4
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable RNA methyltransferase, trmh family (EC 2.1.1.-) | protein | 262 | 40% helix, 21% strand | Q92SJ4 |
| B | Probable RNA methyltransferase, trmh family (EC 2.1.1.-) | protein | 259 | 41% helix, 21% strand | Q92SJ4 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 2 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.68 | 0.79 | 69 | SO4 |
| 2 | 56 | 0.32 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1214 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 5KZK · Crystal Structure of 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 5KZK · PDBe 5KZK · UniProt Q92SJ4
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