MolNFT v1 · #140831 · protein
Crystal structure of an aromatic prenyltransferase FAMD1 from fischerella ambigua utex 1903
5YNT: “Crystal structure of an aromatic prenyltransferase FAMD1 from fischerella ambigua utex 1903”. X-ray diffraction, 1 ligand (DMA), 7 pockets (best druggability 0.81). MolNFT v1 #140831 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YNT
- Type
- protein
- Length
- 612 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic prenyltransferase
- UniProt
- V5TDY7
- Ligands
- DMA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic prenyltransferase | protein | 300 | 37% helix, 25% strand | V5TDY7 |
| B | Aromatic prenyltransferase | protein | 312 | 37% helix, 26% strand | V5TDY7 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · chains A
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 | 345 | 0.81 | 0.91 | 55 | DMA, IMD |
| 2 | 496 | 0.76 | 0.84 | 70 | DMA, IMD |
| 3 | 424 | 0.68 | 0.80 | 46 | empty |
| 4 | 201 | 0.48 | 0.75 | 37 | empty |
| 5 | 51 | 0.39 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 483 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YNT · 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 5YNT · PDBe 5YNT · UniProt V5TDY7
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