Research workbench
Crystal structure of an aromatic prenyltransferase FAMD1 from fischerella ambigua utex 1903 in complex with inn
Analyse Crystal structure of an aromatic prenyltransferase FAMD1 from fischerella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YNU
- Type
- protein
- Length
- 607 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic prenyltransferase
- UniProt
- V5TDY7
- Ligands
- 8XL, POP, DMA
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic prenyltransferase | protein | 296 | 37% helix, 26% strand | V5TDY7 |
| B | Aromatic prenyltransferase | protein | 311 | 37% helix, 26% strand | V5TDY7 |
Ligands and binding sites
- 8XL · 3-[(Z)-2-isocyanoethenyl]-1H-indole · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · chains A
- DMA · Dimethylallyl diphosphate · ligand · chains B
- IMD · Imidazole · additive · 5 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
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 | 333 | 0.81 | 0.91 | 56 | DMA, 8XL |
| 2 | 483 | 0.77 | 0.85 | 63 | 8XL, IMD, POP |
| 3 | 415 | 0.68 | 0.80 | 48 | IMD |
| 4 | 198 | 0.47 | 0.75 | 37 | IMD |
| 5 | 82 | 0.34 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 470 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YNU · 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 5YNU · PDBe 5YNU · UniProt V5TDY7
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