Research workbench
Spinosyn rhamnosyltransferase spng complexed with spinosyn aglycone
Analyse Spinosyn rhamnosyltransferase spng complexed with spinosyn aglycone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UYK
- 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
- 0CX, BGC, MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ndp-rhamnosyltransferase (EC 2.4.1.-) | protein | 373 | 49% helix, 15% strand | Q9ALM8 |
| B | Ndp-rhamnosyltransferase (EC 2.4.1.-) | protein | 369 | 48% helix, 16% strand | Q9ALM8 |
Ligands and binding sites
- 0CX · (2R,3aS,5aR,5bS,9S,13S,14R,16aS,16bR)-9-ethyl-2,13-dihydroxy-14-methyl-2,3,3a,5a,5b,6,9,10,11,12,13,14,16a,16b-tetradecahydro-1H-as-indaceno[3,2-d]oxacyclododecine-7,15-dione · ligand · chains B
- BGC · beta-D-glucopyranose · sugar · chains B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.80 | 0.83 | 80 | 0CX |
| 2 | 685 | 0.80 | 0.84 | 83 | empty |
| 3 | 147 | 0.72 | 0.91 | 33 | empty |
| 4 | 178 | 0.70 | 0.88 | 35 | empty |
| 5 | 84 | 0.45 | 0.80 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1296 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3UYK · Spinosyn Rhamnosyltransferase SpnG complexed with spinosyn aglycone · 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 3UYK · PDBe 3UYK · UniProt Q9ALM8
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