MolNFT v1 · #15346 · protein
(+)-bornyl diphosphate synthase: complex with mg and pyrophosphate
1N1Z: “(+)-bornyl diphosphate synthase: complex with mg and pyrophosphate”. X-ray diffraction, 2 ligands (POP, MG), 19 pockets (best druggability 0.81). MolNFT v1 #15346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1N1Z
- Type
- protein
- Length
- 1,054 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
- POP, MG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (+)-bornyl diphosphate synthase (EC 5.5.1.8) | protein | 537 | 73% helix, 0% strand | O81192 |
| B | (+)-bornyl diphosphate synthase (EC 5.5.1.8) | protein | 517 | 73% helix, 0% strand | O81192 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.81 | 0.97 | 30 | MG, BTB, POP |
| 2 | 399 | 0.79 | 0.88 | 40 | MG, BTB, POP |
| 3 | 636 | 0.77 | 0.83 | 52 | empty |
| 4 | 703 | 0.76 | 0.81 | 58 | empty |
| 5 | 661 | 0.76 | 0.82 | 56 | empty |
Interfaces
1 interface between chains.
- A–B · 1212 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1N1Z · (+)-Bornyl Diphosphate Synthase: Complex with Mg and pyrophosphate · 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 1N1Z · PDBe 1N1Z · UniProt O81192
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