MolNFT v1 · #81669 · protein
Spinosyn rhamnosyltransferase spng complexed with thymidine diphosphate
3UYL · Ndp-rhamnosyltransferase: “Spinosyn rhamnosyltransferase spng complexed with thymidine diphosphate”. X-ray diffraction, 3 ligands (TYD, GLC, MG), 7 pockets (best druggability 0.80). MolNFT v1 #81669 on GenesisL1: 3D structure…
- PDB
- 3UYL
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ndp-rhamnosyltransferase
- EC
- 2.4.1.-
- UniProt
- Q9ALM8
- Ligands
- TYD, GLC, MG
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ndp-rhamnosyltransferase (EC 2.4.1.-) | protein | 372 | 48% helix, 16% strand | Q9ALM8 |
| B | Ndp-rhamnosyltransferase (EC 2.4.1.-) | protein | 370 | 49% helix, 16% strand | Q9ALM8 |
Ligands and binding sites
- TYD · Thymidine-5'-diphosphate · ligand · 2 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.80 | 0.87 | 67 | TYD |
| 2 | 688 | 0.79 | 0.84 | 70 | TYD |
| 3 | 149 | 0.70 | 0.90 | 33 | empty |
| 4 | 123 | 0.65 | 0.89 | 29 | empty |
| 5 | 88 | 0.44 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1304 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3UYL · Spinosyn Rhamnosyltransferase SpnG complexed with thymidine diphosphate · 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 Q9ALM8
- Elsewhere: RCSB PDB 3UYL · PDBe 3UYL · UniProt Q9ALM8
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