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D100E trichodiene synthase: complex with mg, pyrophosphate, and (4S)- 7-azabisabolene
Analyse D100E trichodiene synthase: complex with mg, pyrophosphate, and (4S)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YYU
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trichodiene synthase
- EC
- 4.2.3.6
- UniProt
- P13513
- Ligands
- POP, RAZ, SAZ, MG
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Trichodiene synthase (EC 4.2.3.6) | protein | 354 | 71% helix, 0% strand | P13513 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- RAZ · (1R)-N,4-dimethyl-N-(4-methylpent-3-enyl)cyclohex-3-enaminium · ligand · chains A
- SAZ · (1S)-N,4-dimethyl-N-(4-methylpent-3-enyl)cyclohex-3-enaminium · ligand · chains B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.78 | 0.84 | 67 | MG, SAZ, POP |
| 2 | 99 | 0.78 | 0.98 | 20 | empty |
| 3 | 533 | 0.77 | 0.84 | 55 | MG, RAZ, POP |
| 4 | 66 | 0.75 | 0.99 | 20 | EDO |
| 5 | 403 | 0.63 | 0.78 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 2714 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1YYU · D100E Trichodiene Synthase: Complex With Mg, Pyrophosphate, and (4S)-7-azabisabolene · the same entry in another collection · chain A against A, TM-score 1.00
- P13513 · AlphaFold monomer V2.0 prediction for trichodiene synthase (P13513) · a predicted model of the same protein · 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 P13513
- Elsewhere: RCSB PDB 1YYU · PDBe 1YYU · UniProt P13513
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