MolNFT v1 · #15350 · protein
(+)-bornyl diphosphate synthase: complex with mg, pyrophosphate, and (1R,4S)-2-azabornane
1N23: “(+)-bornyl diphosphate synthase: complex with mg, pyrophosphate, and (1R,4S)-2-azabornane”. X-ray diffraction, 3 ligands (2BN, POP, MG), 18 pockets (best druggability 0.80). MolNFT v1 #15350 on GenesisL1: 3D structure, binding sites…
- PDB
- 1N23
- Type
- protein
- Length
- 1,060 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
- 2BN, POP, MG
- Pockets
- 18 · 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 | 533 | 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
- 2BN · (1R,4S)-2-azabornane · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · 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
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.80 | 0.97 | 31 | MG, 2BN, POP |
| 2 | 672 | 0.76 | 0.82 | 57 | empty |
| 3 | 659 | 0.76 | 0.82 | 57 | empty |
| 4 | 193 | 0.76 | 0.91 | 33 | MG, 2BN, POP |
| 5 | 680 | 0.75 | 0.81 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 1250 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 1N23 · (+)-Bornyl diphosphate synthase: Complex with Mg, pyrophosphate, and (1R,4S)-2-azabornane · 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 1N23 · PDBe 1N23 · UniProt O81192
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