MolNFT v1 · #58001 · protein
Ligand-bound form of arabidopsis MEDIUM/LONG-chain length prenyl pyrophosphate synthase (surface polar residue mutant)
3AQ0 · Geranyl diphosphate synthase: “Ligand-bound form of arabidopsis MEDIUM/LONG-chain length prenyl pyrophosphate synthase (surface polar…”. X-ray diffraction, 4 ligands (FPP, PPV, ISY), 20 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 3AQ0
- Type
- protein
- Length
- 2,551 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyl diphosphate synthase
- EC
- 2.5.1.30
- UniProt
- Q9FT89
- Ligands
- FPP, PPV, ISY, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 326 | 72% helix, 1% strand | Q9FT89 |
| B | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 313 | 73% helix, 0% strand | Q9FT89 |
| C | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 327 | 74% helix, 1% strand | Q9FT89 |
| D | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 312 | 75% helix, 0% strand | Q9FT89 |
| E | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 325 | 74% helix, 1% strand | Q9FT89 |
| F | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 310 | 74% helix, 0% strand | Q9FT89 |
| G | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 314 | 71% helix, 0% strand | Q9FT89 |
| H | Geranyl diphosphate synthase (EC 2.5.1.30) | protein | 324 | 73% helix, 1% strand | Q9FT89 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · 6 copies · chains A, B, F, C, D, E, G, H
- PPV · Pyrophosphate · ligand · 6 copies · chains B, C, D, E, F, G
- ISY · 3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid · ligand · 2 copies · chains A, H
- MG · Magnesium ion · metal · 8 copies · chains A, C, E, H
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains B, E, F, C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 882 | 0.87 | 0.88 | 114 | PEG, PPV |
| 2 | 993 | 0.82 | 0.83 | 98 | empty |
| 3 | 720 | 0.82 | 0.85 | 78 | MG, FPP, PPV |
| 4 | 976 | 0.82 | 0.83 | 93 | empty |
| 5 | 913 | 0.81 | 0.83 | 76 | MG, FPP, PPV |
Interfaces
16 interfaces between chains.
- D–G · 3255 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 3058 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1777 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1741 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1608 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3AQ0 · Ligand-bound form of Arabidopsis medium/long-chain length prenyl pyrophosphate synthase… · the same entry in another collection · 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 Q9FT89
- Elsewhere: RCSB PDB 3AQ0 · PDBe 3AQ0 · UniProt Q9FT89
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