Research workbench
Crystal structure of gamma-terpinene synthase from thymus vulgaris
Analyse Crystal structure of gamma-terpinene synthase from thymus vulgaris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C05
- Type
- protein
- Length
- 1,036 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative gamma-terpinene synthase
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative gamma-terpinene synthase | protein | 514 | 73% helix, 0% strand | — |
| B | Putative gamma-terpinene synthase | protein | 522 | 74% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 8 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.76 | 0.83 | 46 | EDO |
| 2 | 580 | 0.75 | 0.82 | 44 | EDO |
| 3 | 662 | 0.70 | 0.77 | 42 | empty |
| 4 | 341 | 0.69 | 0.82 | 35 | empty |
| 5 | 547 | 0.69 | 0.78 | 51 | EDO |
Interfaces
1 interface between chains.
- A–B · 1181 Ų buried · 11 hydrogen bonds · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5C05 · PDBe 5C05
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