MolNFT v1 · #15347 · protein
(+)-bornyl diphosphate synthase: complex with mg and 3-aza- 2,3-dihydrogeranyl diphosphate
1N20: “(+)-bornyl diphosphate synthase: complex with mg and 3-aza- 2,3-dihydrogeranyl diphosphate”. X-ray diffraction, 2 ligands (3AG, MG), 17 pockets (best druggability 0.80). MolNFT v1 #15347 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1N20
- Type
- protein
- Length
- 1,059 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (+)-bornyl diphosphate synthase
- EC
- 5.5.1.8
- UniProt
- O81192
- Ligands
- 3AG, MG
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (+)-bornyl diphosphate synthase (EC 5.5.1.8) | protein | 532 | 72% helix, 0% strand | O81192 |
| B | (+)-bornyl diphosphate synthase (EC 5.5.1.8) | protein | 527 | 72% helix, 0% strand | O81192 |
Ligands and binding sites
- 3AG · 2-[methyl-(4-methyl-pent-3-enyl)-amino]-ethyl-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.80 | 0.95 | 33 | 3AG |
| 2 | 212 | 0.77 | 0.92 | 35 | MG, 3AG |
| 3 | 678 | 0.76 | 0.82 | 56 | empty |
| 4 | 659 | 0.76 | 0.81 | 50 | empty |
| 5 | 677 | 0.75 | 0.81 | 55 | empty |
Interfaces
1 interface between chains.
- A–B · 1211 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1N20 · (+)-Bornyl Diphosphate Synthase: Complex with Mg and 3-aza-2,3-dihydrogeranyl diphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- O81192 · AlphaFold monomer V2.0 prediction for (+)-bornyl diphosphate synthase, chloroplastic… · a predicted model of the same protein · 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 O81192
- Elsewhere: RCSB PDB 1N20 · PDBe 1N20 · UniProt O81192
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