Research workbench
Streptomyces spheroides novo (8-demethylnovbiocic acid methyltransferase) with sah
Analyse Streptomyces spheroides novo (8-demethylnovbiocic acid methyltransferase) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MGZ
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8-demethylnovobiocic acid C(8)-methyltransferase
- EC
- 2.1.1.284
- UniProt
- Q9L9F3
- Ligands
- SAH
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 8-demethylnovobiocic acid C(8)-methyltransferase (EC 2.1.1.284) | protein | 230 | 44% helix, 22% strand | Q9L9F3 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.84 | 0.95 | 42 | SAH, GOL, ACT |
| 2 | 311 | 0.83 | 0.93 | 47 | SAH |
| 3 | 74 | 0.50 | 0.84 | 17 | empty |
| 4 | 89 | 0.50 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 887 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5MGZ · Streptomyces Spheroides NovO (8-demethylnovbiocic acid methyltransferase) with SAH · the same entry in another collection · chain A against A, TM-score 1.00
- Q9L9F3 · AlphaFold monomer V2.0 prediction for 8-demethylnovobiocic acid C(8)-methyltransferase… · a predicted model of the same protein · chain A 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 Q9L9F3
- Elsewhere: RCSB PDB 5MGZ · PDBe 5MGZ · UniProt Q9L9F3
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