MolNFT v1 · #74742 · protein
Crystal structure of taxadiene synthase from pacific yew (taxus brevifolia) in complex with MG2+ and 13-aza-13,14-dihydrocopalyl diphosphate
3P5P: “Crystal structure of taxadiene synthase from pacific yew (taxus brevifolia) in complex with MG2+ and…”. X-ray diffraction, 2 ligands (A3C, MG), 9 pockets (best druggability 0.75). MolNFT v1 #74742 on GenesisL1: 3D structure, binding…
- PDB
- 3P5P
- Type
- protein
- Length
- 745 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Taxadiene synthase
- EC
- 4.2.3.17
- UniProt
- Q41594
- Ligands
- A3C, MG
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taxadiene synthase (EC 4.2.3.17) | protein | 745 | 66% helix, 2% strand | Q41594 |
Ligands and binding sites
- A3C · 2-(methyl{2-[(1S,4aS,8aS)-5,5,8a-trimethyl-2-methylidenedecahydronaphthalen-1-yl]ethyl}amino)ethyl trihydrogen diphosphate · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.75 | 0.83 | 48 | MG, A3C |
| 2 | 539 | 0.75 | 0.83 | 46 | EDO |
| 3 | 418 | 0.72 | 0.82 | 50 | EDO |
| 4 | 302 | 0.61 | 0.79 | 30 | empty |
| 5 | 58 | 0.49 | 0.85 | 19 | empty |
Compared structures
- 3P5P · 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 A against A, TM-score 0.99
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 3P5P · PDBe 3P5P · UniProt Q41594
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