MolNFT v1 · #125953 · protein
Crystal structure of safc from myxococcus xanthus bound to SAM
5LOG · Putative O-methyltransferase: “Crystal structure of safc from myxococcus xanthus bound to SAM”. X-ray diffraction, 4 ligands (SAH, LDP, MG), 4 pockets (best druggability 0.67). MolNFT v1 #125953 on GenesisL1: 3D structure, binding…
- PDB
- 5LOG
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative O-methyltransferase
- UniProt
- Q50859
- Ligands
- SAH, LDP, MG, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative O-methyltransferase | protein | 222 | 46% helix, 20% strand | Q50859 |
| B | Putative O-methyltransferase | protein | 218 | 46% helix, 21% strand | Q50859 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- LDP · L-dopamine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.67 | 0.79 | 59 | SAH, LDP |
| 2 | 290 | 0.66 | 0.82 | 43 | empty |
| 3 | 155 | 0.53 | 0.80 | 21 | empty |
| 4 | 132 | 0.53 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2528 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5LOG · Crystal Structure of SafC from Myxococcus xanthus bound to SAM · 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 Q50859
- Elsewhere: RCSB PDB 5LOG · PDBe 5LOG · UniProt Q50859
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.