MolNFT v1 · #127734 · protein
Crystal structure of the O-methyltransferase tomg from streptomyces achromogenes involved in tomaymycin synthesis in complex with SAM
5N5D: “Crystal structure of the O-methyltransferase tomg from streptomyces achromogenes involved in tomaymycin…”. X-ray diffraction, 2 ligands (SAM, SO4), 5 pockets (best druggability 0.63). MolNFT v1 #127734 on GenesisL1: 3D structure…
- PDB
- 5N5D
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase
- UniProt
- A0A0J8AIC3
- Ligands
- SAM, SO4
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methyltransferase | protein | 224 | 45% helix, 20% strand | A0A0J8AIC3 |
| B | Methyltransferase | protein | 223 | 47% helix, 22% strand | A0A0J8AIC3 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- BU3 · (R,R)-2,3-butanediol · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.63 | 0.82 | 51 | BU3, SAM |
| 2 | 140 | 0.47 | 0.78 | 29 | SAM |
| 3 | 66 | 0.34 | 0.77 | 17 | BU3 |
| 4 | 56 | 0.28 | 0.74 | 14 | BU3 |
| 5 | 54 | 0.25 | 0.72 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2175 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5N5D · Crystal Structure of the O-Methyltransferase TomG from Streptomyces achromogenes involved… · 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 A0A0J8AIC3
- Elsewhere: RCSB PDB 5N5D · PDBe 5N5D · UniProt A0A0J8AIC3
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