Research workbench
D100E trichodiene synthase complexed with pyrophosphate
Analyse D100E trichodiene synthase complexed with pyrophosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KIZ
- Type
- protein
- Length
- 708 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trichodiene synthase
- EC
- 4.1.99.6
- UniProt
- P13513
- Ligands
- POP, MG
- Pockets
- 12 · 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 4.1.99.6) | protein | 354 | 71% helix, 0% strand | P13513 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.78 | 0.85 | 46 | MG, POP, EDO |
| 2 | 96 | 0.77 | 0.98 | 20 | empty |
| 3 | 528 | 0.77 | 0.84 | 46 | EDO |
| 4 | 59 | 0.73 | 0.98 | 19 | EDO |
| 5 | 291 | 0.61 | 0.79 | 40 | empty |
Interfaces
1 interface between chains.
- A–B · 2767 Ų buried · 28 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 1KIZ · PDBe 1KIZ · UniProt P13513
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