Research workbench
Crystal structure of the aromatic prenyltransferase atapt from aspergillus terreus A8-4 in complex with dimethylallyl S- thiolodiphosphate and (-)-butyrolactone II
Analyse Crystal structure of the aromatic prenyltransferase atapt from aspergillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KD6
- Type
- protein
- Length
- 799 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aromatic prenyltransferase
- Ligands
- DST, LBU
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aromatic prenyltransferase | protein | 400 | 43% helix, 20% strand | — |
| B | Aromatic prenyltransferase | protein | 399 | 44% helix, 20% strand | — |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- LBU · methyl (2S)-4-hydroxy-3-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-5-oxo-2,5-dihydrofuran-2-carboxylate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.81 | 0.82 | 90 | DST |
| 2 | 944 | 0.81 | 0.82 | 82 | LBU, DST |
| 3 | 73 | 0.73 | 0.98 | 21 | empty |
| 4 | 66 | 0.71 | 0.97 | 23 | empty |
| 5 | 79 | 0.53 | 0.85 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1412 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5KD6 · 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 5KD6 · PDBe 5KD6
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