MolNFT v1 · #20807 · protein
Active conformation of farnesyl pyrophosphate synthase bound to isopentyl pyrophosphate and dimethylallyl S-thiolodiphosphate
1RQI · Geranyltranstransferase: “Active conformation of farnesyl pyrophosphate synthase bound to isopentyl pyrophosphate and dimethylallyl…”. X-ray diffraction, 4 ligands (DST, IPR, DPO), 5 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 1RQI
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyltranstransferase
- EC
- 2.5.1.10
- UniProt
- P22939
- Ligands
- DST, IPR, DPO, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyltranstransferase (EC 2.5.1.10) | protein | 300 | 74% helix, 1% strand | P22939 |
| B | Geranyltranstransferase (EC 2.5.1.10) | protein | 298 | 74% helix, 1% strand | P22939 |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- IPR · Isopentyl pyrophosphate · ligand · 2 copies · chains A, B
- DPO · Diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.80 | 0.91 | 46 | MG, DST, IPR |
| 2 | 313 | 0.79 | 0.90 | 47 | MG, DST, IPR |
| 3 | 78 | 0.40 | 0.78 | 17 | empty |
| 4 | 68 | 0.37 | 0.78 | 12 | DPO |
| 5 | 56 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1857 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 1RQI · Active Conformation of Farnesyl Pyrophosphate Synthase Bound to Isopentyl Pyrophosphate… · the same entry in another collection · chain A against A, TM-score 1.00
- P22939 · AlphaFold monomer V2.0 prediction for farnesyl diphosphate synthase (P22939) · a predicted model of the same protein · chain B 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 P22939
- Elsewhere: RCSB PDB 1RQI · PDBe 1RQI · UniProt P22939
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