MolNFT v1 · #69463 · protein
Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium
3KRA · Geranyl diphosphate synthase large subunit: “Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium”. X-ray diffraction, 1 ligand (MG), 14 pockets (best druggability 0.75). MolNFT v1 #69463 on GenesisL1: 3D…
- PDB
- 3KRA
- 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
- MG
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 72% 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 | 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 | 73% helix, 1% strand | Q9SBR3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.75 | 0.78 | 90 | MG |
| 2 | 388 | 0.67 | 0.80 | 44 | empty |
| 3 | 397 | 0.66 | 0.79 | 34 | empty |
| 4 | 428 | 0.63 | 0.77 | 42 | empty |
| 5 | 266 | 0.55 | 0.77 | 35 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2043 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2013 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 452 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 432 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 85 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3KRA · Mint heterotetrameric geranyl pyrophosphate synthase in complex with magnesium · 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 3KRA · PDBe 3KRA · UniProt Q9SBR3 · UniProt Q9SBR4
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