MolNFT v1 · #123561 · protein
Henbane premnaspirodiene synthase (hps), also known as henbane vetispiradiene synthase (hvs) from hyoscyamus muticus
5JO7 · Vetispiradiene synthase 1: “Henbane premnaspirodiene synthase (hps), also known as henbane vetispiradiene synthase (hvs) from hyoscyamus…”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #123561 on GenesisL1: 3D…
- PDB
- 5JO7
- Type
- protein
- Length
- 2,018 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vetispiradiene synthase 1
- EC
- 4.2.3.21
- UniProt
- Q39978
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vetispiradiene synthase 1 (EC 4.2.3.21) | protein | 510 | 76% helix, 0% strand | Q39978 |
| B | Vetispiradiene synthase 1 (EC 4.2.3.21) | protein | 506 | 75% helix, 0% strand | Q39978 |
| C | Vetispiradiene synthase 1 (EC 4.2.3.21) | protein | 503 | 74% helix, 0% strand | Q39978 |
| D | Vetispiradiene synthase 1 (EC 4.2.3.21) | protein | 499 | 73% helix, 0% strand | Q39978 |
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.83 | 0.90 | 55 | empty |
| 2 | 474 | 0.83 | 0.90 | 50 | empty |
| 3 | 522 | 0.82 | 0.89 | 53 | empty |
| 4 | 545 | 0.82 | 0.88 | 44 | empty |
| 5 | 1147 | 0.79 | 0.80 | 94 | empty |
Interfaces
5 interfaces between chains.
- A–B · 956 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 849 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 223 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 82 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JO7 · Henbane premnaspirodiene synthase (HPS), also known as Henbane vetispiradiene synthase… · the same entry in another collection · chain D against D, TM-score 1.00
- Q39978 · AlphaFold monomer V2.0 prediction for vetispiradiene synthase 1 (Q39978) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q39978
- Elsewhere: RCSB PDB 5JO7 · PDBe 5JO7 · UniProt Q39978
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