Research workbench
Crystal structure of the sesquiterpene synthase COPU9 from coniophora puteana in complex with alendronate
Analyse Crystal structure of the sesquiterpene synthase COPU9 from coniophora puteana… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OFL
- Type
- protein
- Length
- 669 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terpene synthase
- EC
- 4.2.3.-
- UniProt
- A0A5M3MXY8
- Ligands
- AHD, MG
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Terpene synthase (EC 4.2.3.-) | protein | 335 | 69% helix, 2% strand | A0A5M3MXY8 |
| B | Terpene synthase (EC 4.2.3.-) | protein | 334 | 67% helix, 2% strand | A0A5M3MXY8 |
Ligands and binding sites
- AHD · 4-amino-1-hydroxybutane-1,1-diyldiphosphonate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.81 | 0.96 | 31 | AHD, MG, EDO |
| 2 | 781 | 0.81 | 0.84 | 67 | EDO |
| 3 | 392 | 0.78 | 0.88 | 56 | AHD, MG |
| 4 | 176 | 0.51 | 0.78 | 25 | empty |
| 5 | 145 | 0.41 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 505 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7OFL · Crystal structure of the sesquiterpene synthase Copu9 from coniophora puteana in complex… · the same entry in another collection · 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 A0A5M3MXY8
- Elsewhere: RCSB PDB 7OFL · PDBe 7OFL · UniProt A0A5M3MXY8
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