MolNFT v1 · #135493 · protein
Crystal structure of a methyltransferase in complex with the substrate involved in the biosynthesis of gentamicin
5U0N · Putative gentamicin methyltransferase: “Crystal structure of a methyltransferase in complex with the substrate involved in the biosynthesis of…”. X-ray diffraction, 3 ligands (SAH, 7XP, MG), 2 pockets (best druggability 0.71).…
- PDB
- 5U0N
- Type
- protein
- Length
- 307 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative gentamicin methyltransferase
- UniProt
- Q2MG72
- Ligands
- SAH, 7XP, MG
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative gentamicin methyltransferase | protein | 307 | 32% helix, 29% strand | Q2MG72 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- 7XP · (1R,2S,3S,4R,6S)-4,6-diamino-3-[(3-amino-3-deoxy-alpha-D-xylopyranosyl)oxy]-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside · ligand · chains A
- MG · Magnesium ion · metal · 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 | 293 | 0.71 | 0.85 | 49 | SAH, 7XP |
| 2 | 70 | 0.33 | 0.75 | 19 | empty |
Compared structures
- 5U0N · Crystal structure of a methyltransferase in complex with the substrate involved in the… · 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 5U0N · PDBe 5U0N · UniProt Q2MG72
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