Research workbench
Mint heterotetrameric geranyl pyrophosphate synthase in complex with ipp
Analyse Mint heterotetrameric geranyl pyrophosphate synthase in complex with ipp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KRC
- Type
- protein
- Length
- 1,086 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
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyl diphosphate synthase large subunit (EC 2.5.1.1) | protein | 279 | 76% helix, 1% strand | Q9SBR3 |
| B | Geranyl diphosphate synthase small subunit (EC 2.5.1.1) | protein | 259 | 69% helix, 0% strand | Q9SBR4 |
| C | Geranyl diphosphate synthase small subunit (EC 2.5.1.1) | protein | 271 | 69% helix, 0% strand | Q9SBR4 |
| D | Geranyl diphosphate synthase large subunit (EC 2.5.1.1) | protein | 277 | 74% helix, 1% strand | Q9SBR3 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, D
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.72 | 0.77 | 78 | IPE |
| 2 | 59 | 0.71 | 0.98 | 26 | empty |
| 3 | 359 | 0.68 | 0.82 | 46 | empty |
| 4 | 476 | 0.68 | 0.79 | 46 | empty |
| 5 | 383 | 0.64 | 0.79 | 45 | IPE |
Interfaces
6 interfaces between chains.
- A–B · 2026 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2025 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 480 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 439 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 84 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3KRC · Mint heterotetrameric geranyl pyrophosphate synthase in complex with IPP · 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 3KRC · PDBe 3KRC · UniProt Q9SBR3 · UniProt Q9SBR4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.