MolNFT v1 · #140834 · protein
Crystal structure of an aromatic prenyltransferase FAMD1 from fischerella ambigua utex 1903 in complex with dmaspp and inn
5YNW: “Crystal structure of an aromatic prenyltransferase FAMD1 from fischerella ambigua utex 1903 in complex with…”. X-ray diffraction, 2 ligands (DST, 8XL), 6 pockets (best druggability 0.84). MolNFT v1 #140834 on GenesisL1: 3D…
- PDB
- 5YNW
- Type
- protein
- Length
- 613 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic prenyltransferase
- UniProt
- V5TDY7
- Ligands
- DST, 8XL
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic prenyltransferase | protein | 301 | 37% helix, 25% strand | V5TDY7 |
| B | Aromatic prenyltransferase | protein | 312 | 38% helix, 27% strand | V5TDY7 |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- 8XL · 3-[(Z)-2-isocyanoethenyl]-1H-indole · ligand · chains B
- GOL · Glycerol · additive · chains A
- IMD · Imidazole · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.84 | 0.95 | 48 | 8XL, DST |
| 2 | 456 | 0.78 | 0.86 | 60 | DST, IMD |
| 3 | 417 | 0.68 | 0.80 | 50 | empty |
| 4 | 191 | 0.48 | 0.75 | 37 | empty |
| 5 | 73 | 0.33 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YNW · Crystal structure of an aromatic prenyltransferase FAMD1 from Fischerella ambigua UTEX… · 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 V5TDY7
- Elsewhere: RCSB PDB 5YNW · PDBe 5YNW · UniProt V5TDY7
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