Research workbench
Mint deletion mutant of heterotetrameric geranyl pyrophosphate synthase in complex with ligands
Analyse Mint deletion mutant of heterotetrameric geranyl pyrophosphate synthase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OAC
- Type
- protein
- Length
- 1,070 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyl diphosphate synthase large subunit; Geranyl diphosphate synthase small subunit
- EC
- 2.5.1.1
- UniProt
- Q9SBR3, Q9SBR4
- Ligands
- IPE, DST, MG
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyl diphosphate synthase large subunit (EC 2.5.1.1) | protein | 279 | 75% helix, 1% strand | Q9SBR3 |
| B, C | Geranyl diphosphate synthase small subunit (EC 2.5.1.1) | protein | 248 | 72% helix, 0% strand | Q9SBR4 |
| D | Geranyl diphosphate synthase large subunit (EC 2.5.1.1) | protein | 295 | 73% helix, 1% strand | Q9SBR3 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains D
- DST · Dimethylallyl S-thiolodiphosphate · ligand · chains D
- MG · Magnesium ion · metal · 2 copies · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.82 | 0.91 | 52 | IPE, DST, MG |
| 2 | 146 | 0.66 | 0.87 | 30 | empty |
| 3 | 466 | 0.63 | 0.76 | 69 | empty |
| 4 | 174 | 0.63 | 0.84 | 36 | empty |
| 5 | 343 | 0.62 | 0.78 | 33 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1876 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1844 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 459 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 447 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 91 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3OAC · Mint deletion mutant of heterotetrameric geranyl pyrophosphate synthase in complex with… · 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 Q9SBR3
- Every structure of UniProt Q9SBR4
- Elsewhere: RCSB PDB 3OAC · PDBe 3OAC · UniProt Q9SBR3 · UniProt Q9SBR4
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