MolNFT v1 · #124371 · protein
Crystal structure of the aromatic prenyltransferase atapt from aspergillus terreus A8-4 in complex with dimethylallyl S- thiolodiphosphate and genistein
5KDA: “Crystal structure of the aromatic prenyltransferase atapt from aspergillus terreus A8-4 in complex with…”. X-ray diffraction, 2 ligands (DST, GEN), 8 pockets (best druggability 0.82). MolNFT v1 #124371 on GenesisL1: 3D structure…
- PDB
- 5KDA
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic prenyltransferase
- Ligands
- DST, GEN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic prenyltransferase | protein | 400 | 44% helix, 20% strand | — |
| B | Aromatic prenyltransferase | protein | 397 | 43% helix, 19% strand | — |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- GEN · Genistein · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.82 | 0.83 | 84 | GEN, DST |
| 2 | 1003 | 0.81 | 0.82 | 80 | DST |
| 3 | 76 | 0.73 | 0.97 | 21 | empty |
| 4 | 66 | 0.71 | 0.97 | 21 | empty |
| 5 | 120 | 0.54 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1400 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5KDA · Crystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4… · 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
- Elsewhere: RCSB PDB 5KDA · PDBe 5KDA
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