MolNFT v1 · #99595 · protein
Ensemble refinement of protein crystal structure (2IYF) of macrolide glycosyltransferases oled complexed with udp and erythromycin a
4M83 · Oleandomycin glycosyltransferase: “Ensemble refinement of protein crystal structure (2IYF) of macrolide glycosyltransferases oled complexed with…”. X-ray diffraction, 3 ligands (ERY, UDP, MG), 7 pockets (best druggability 0.77).…
- PDB
- 4M83
- Type
- protein
- Length
- 787 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oleandomycin glycosyltransferase
- UniProt
- Q3HTL6
- Ligands
- ERY, UDP, MG
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oleandomycin glycosyltransferase | protein | 393 | 45% helix, 14% strand | Q3HTL6 |
| B | Oleandomycin glycosyltransferase | protein | 394 | 45% 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
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1176 | 0.77 | 0.79 | 124 | ERY, UDP |
| 2 | 482 | 0.68 | 0.79 | 56 | ERY |
| 3 | 433 | 0.59 | 0.75 | 50 | UDP |
| 4 | 201 | 0.48 | 0.75 | 26 | empty |
| 5 | 84 | 0.47 | 0.82 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 597 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4M83 · Ensemble refinement of protein crystal structure (2IYF) of macrolide glycosyltransferases… · 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 4M83 · PDBe 4M83 · UniProt Q3HTL6
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