Research workbench
The crystal structure of macrolide glycosyltransferases: a blueprint for antibiotic engineering
Analyse The crystal structure of macrolide glycosyltransferases: a blueprint for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IYF
- Type
- protein
- Length
- 778 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oleandomycin glycosyltransferase
- EC
- 2.4.1.-
- UniProt
- Q3HTL6
- Ligands
- ERY, UDP, MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oleandomycin glycosyltransferase (EC 2.4.1.-) | protein | 384 | 48% helix, 15% strand | Q3HTL6 |
| B | Oleandomycin glycosyltransferase (EC 2.4.1.-) | protein | 394 | 47% helix, 14% strand | Q3HTL6 |
Ligands and binding sites
- ERY · Erythromycin A · ligand · 2 copies · chains A, B
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.71 | 0.82 | 46 | ERY |
| 2 | 680 | 0.70 | 0.77 | 78 | UDP |
| 3 | 466 | 0.67 | 0.79 | 44 | ERY |
| 4 | 313 | 0.52 | 0.74 | 42 | UDP |
| 5 | 196 | 0.48 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 601 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2IYF · The crystal structure of macrolide glycosyltransferases: A blueprint for antibiotic… · 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 Q3HTL6
- Elsewhere: RCSB PDB 2IYF · PDBe 2IYF · UniProt Q3HTL6
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