MolNFT v1 · #102414 · protein
Selinadiene synthase in complex with dihydrofarnesyl pyrophosphate
4OKZ · Terpene synthase metal-binding domain-containing protein: “Selinadiene synthase in complex with dihydrofarnesyl pyrophosphate”. X-ray diffraction, 2 ligands (3E9, MG), 12 pockets (best druggability 0.87). MolNFT v1 #102414 on…
- PDB
- 4OKZ
- Type
- protein
- Length
- 1,382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Terpene synthase metal-binding domain-containing protein
- EC
- 2.5.1.21
- UniProt
- B5HDJ6
- Ligands
- 3E9, MG
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Terpene synthase metal-binding domain-containing protein (EC 2.5.1.21) | protein | 346 | 68% helix, 1% strand | B5HDJ6 |
| B, C | Terpene synthase metal-binding domain-containing protein (EC 2.5.1.21) | protein | 345 | 68% helix, 1% strand | B5HDJ6 |
Ligands and binding sites
- 3E9 · (3S,6E)-3,7,11-trimethyldodeca-6,10-dien-1-yl trihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.87 | 0.93 | 71 | empty |
| 2 | 518 | 0.86 | 0.92 | 68 | empty |
| 3 | 216 | 0.82 | 0.96 | 36 | MG, 3E9 |
| 4 | 210 | 0.82 | 0.96 | 35 | MG, 3E9 |
| 5 | 204 | 0.82 | 0.95 | 37 | MG, 3E9 |
Interfaces
4 interfaces between chains.
- C–D · 1979 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1965 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 859 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OKZ · Selinadiene Synthase in complex with dihydrofarnesyl pyrophosphate · the same entry in another collection · chain B against B, TM-score 1.00
- B5HDJ6 · AlphaFold monomer V2.0 prediction for selina-4(15),7(11)-diene synthase ((2E,6E)-farnesyl… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 B5HDJ6
- Elsewhere: RCSB PDB 4OKZ · PDBe 4OKZ · UniProt B5HDJ6
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