Research workbench
Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in complex with the kanamycin B
Analyse Crystal structure of a methyltransferase involved in the biosynthesis of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U1E
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.213
- Source
- Micromonospora echinospora
- Molecule
- Putative gentamicin methyltransferase
- UniProt
- Q2MG72
- Ligands
- 9CS, SAH
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · resolution 2.213 · 1 distinct chain · 35% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative gentamicin methyltransferase | protein | 321 | 35% helix, 28% strand | Q2MG72 |
Ligands and binding sites
- 9CS · (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-2-hydroxycyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
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 | 268 | 0.71 | 0.85 | 44 | 9CS, SAH |
| 2 | 53 | 0.41 | 0.82 | 15 | empty |
Compared structures
- 5U1E · Crystal structure of a methyltransferase involved in the biosynthesis of gentamicin in… · 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 Q2MG72
- Elsewhere: RCSB PDB 5U1E · PDBe 5U1E · UniProt Q2MG72
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