Research workbench
Crystal structure of taxadiene synthase from pacific yew (taxus brevifolia) in complex with MG2+ and 2-fluorogeranylgeranyl diphosphate
Analyse Crystal structure of taxadiene synthase from pacific yew (taxus brevifolia) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P5R
- Type
- protein
- Length
- 1,488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Taxadiene synthase
- EC
- 4.2.3.17
- UniProt
- Q41594
- Ligands
- FGG, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taxadiene synthase (EC 4.2.3.17) | protein | 750 | 64% helix, 2% strand | Q41594 |
| B | Taxadiene synthase (EC 4.2.3.17) | protein | 738 | 65% helix, 2% strand | Q41594 |
Ligands and binding sites
- FGG · (2Z,6E,10E)-2-fluoro-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.79 | 0.86 | 53 | empty |
| 2 | 594 | 0.77 | 0.84 | 57 | empty |
| 3 | 476 | 0.76 | 0.84 | 38 | MG, FGG |
| 4 | 406 | 0.74 | 0.84 | 35 | MG, FGG |
| 5 | 394 | 0.73 | 0.84 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3P5R · Crystal Structure of Taxadiene Synthase from Pacific Yew (Taxus brevifolia) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q41594 · AlphaFold monomer V2.0 prediction for taxadiene synthase (Q41594) · a predicted model of the same protein · chain B 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 Q41594
- Elsewhere: RCSB PDB 3P5R · PDBe 3P5R · UniProt Q41594
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