MolNFT v1 · #126514 · protein
Crystal structure of couo, a C-methyltransferase from streptomyces rishiriensis
5M58 · C-methyltransferase couo: “Crystal structure of couo, a C-methyltransferase from streptomyces rishiriensis”. X-ray diffraction, 1 ligand (SAH), 3 pockets (best druggability 0.83). MolNFT v1 #126514 on GenesisL1: 3D structure…
- PDB
- 5M58
- Type
- protein
- Length
- 459 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-methyltransferase couo
- EC
- 2.1.1.-
- UniProt
- Q9F8T9
- Ligands
- SAH
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-methyltransferase couo (EC 2.1.1.-) | protein | 230 | 46% helix, 22% strand | Q9F8T9 |
| B | C-methyltransferase couo (EC 2.1.1.-) | protein | 229 | 47% helix, 22% strand | Q9F8T9 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.83 | 0.94 | 41 | SAH |
| 2 | 258 | 0.80 | 0.92 | 50 | SAH |
| 3 | 450 | 0.67 | 0.79 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 325 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5M58 · Crystal structure of CouO, a C-methyltransferase from Streptomyces rishiriensis · the same entry in another collection · chain B against B, TM-score 1.00
- Q9F8T9 · AlphaFold monomer V2.0 prediction for C-methyltransferase couo (Q9F8T9) · a predicted model of the same protein · chain B 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 Q9F8T9
- Elsewhere: RCSB PDB 5M58 · PDBe 5M58 · UniProt Q9F8T9
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