MolNFT v1 · #29119 · protein
Y305F trichodiene synthase complexed with pyrophosphate
1YYQ: “Y305F trichodiene synthase complexed with pyrophosphate”. X-ray diffraction, 2 ligands (POP, MG), 12 pockets (best druggability 0.84). MolNFT v1 #29119 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YYQ
- Type
- protein
- Length
- 704 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, MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trichodiene synthase (EC 4.2.3.6) | protein | 353 | 71% helix, 0% strand | P13513 |
| B | Trichodiene synthase (EC 4.2.3.6) | protein | 351 | 71% helix, 0% strand | P13513 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.84 | 0.97 | 35 | MG, POP |
| 2 | 82 | 0.77 | 0.99 | 21 | empty |
| 3 | 609 | 0.76 | 0.82 | 47 | empty |
| 4 | 65 | 0.75 | 0.98 | 19 | empty |
| 5 | 307 | 0.59 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 2757 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
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 1YYQ · PDBe 1YYQ · UniProt P13513
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