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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
- 2IYA
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oleandomycin glycosyltransferase
- EC
- 2.4.1.-
- UniProt
- Q3HTL7
- Ligands
- UDP, ZIO
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oleandomycin glycosyltransferase (EC 2.4.1.-) | protein | 392 | 46% helix, 14% strand | Q3HTL7 |
| B | Oleandomycin glycosyltransferase (EC 2.4.1.-) | protein | 384 | 46% helix, 14% strand | Q3HTL7 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- ZIO · (3S,5R,6S,7R,8R,11R,12S,13R,14S,15S)-6-hydroxy-5,7,8,11,13,15-hexamethyl-4,10-dioxo-14-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}-1,9-dioxaspiro[2.13]hexadec-12-yl 2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranoside · ligand · 2 copies · chains A, 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 | 733 | 0.86 | 0.89 | 64 | UDP, ZIO |
| 2 | 861 | 0.85 | 0.87 | 87 | UDP, ZIO |
| 3 | 270 | 0.60 | 0.79 | 36 | empty |
| 4 | 291 | 0.56 | 0.76 | 35 | empty |
| 5 | 151 | 0.49 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 914 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 2IYA · 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 Q3HTL7
- Elsewhere: RCSB PDB 2IYA · PDBe 2IYA · UniProt Q3HTL7
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