MolNFT v1 · #40736 · protein
Geranylgeranyl diphosphate synthase from sinapis alba in complex with ggpp
2J1P · Geranylgeranyl pyrophosphate synthetase: “Geranylgeranyl diphosphate synthase from sinapis alba in complex with ggpp”. X-ray diffraction, 1 ligand (GRG), 7 pockets (best druggability 0.71). MolNFT v1 #40736 on GenesisL1: 3D…
- PDB
- 2J1P
- Type
- protein
- Length
- 553 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranylgeranyl pyrophosphate synthetase
- UniProt
- Q43133
- Ligands
- GRG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranylgeranyl pyrophosphate synthetase | protein | 276 | 75% helix, 1% strand | Q43133 |
| B | Geranylgeranyl pyrophosphate synthetase | protein | 277 | 74% helix, 1% strand | Q43133 |
Ligands and binding sites
- GRG · Geranylgeranyl diphosphate · ligand · chains A, B
- PGO · S-1,2-propanediol · additive · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.71 | 0.80 | 61 | GRG |
| 2 | 488 | 0.67 | 0.78 | 51 | BME |
| 3 | 62 | 0.45 | 0.83 | 17 | empty |
| 4 | 131 | 0.44 | 0.76 | 18 | empty |
| 5 | 58 | 0.41 | 0.81 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1647 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2J1P · Geranylgeranyl diphosphate synthase from Sinapis alba in complex with GGPP · the same entry in another collection · chain A against A, TM-score 1.00
- Q43133 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q43133
- Elsewhere: RCSB PDB 2J1P · PDBe 2J1P · UniProt Q43133
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