Research workbench
Crystal structure of upps in complex with fpp and an allosteric inhibitor
Analyse Crystal structure of upps in complex with fpp and an allosteric inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q9M
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoprenyl transferase
- EC
- 2.5.1.-
- UniProt
- Q8DRB3
- Ligands
- 2ZW, FPP, CD
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoprenyl transferase (EC 2.5.1.-) | protein | 230 | 52% helix, 15% strand | Q8DRB3 |
| B | Isoprenyl transferase (EC 2.5.1.-) | protein | 228 | 51% helix, 15% strand | Q8DRB3 |
Ligands and binding sites
- 2ZW · 3-(2-chlorophenyl)-5-methyl-N-[4-(propan-2-yl)phenyl]-1,2-oxazole-4-carboxamide · ligand · 2 copies · chains A, B
- FPP · Farnesyl diphosphate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.83 | 0.91 | 44 | 2ZW, FPP, CD |
| 2 | 454 | 0.83 | 0.90 | 47 | 2ZW, FPP, CD |
| 3 | 78 | 0.75 | 0.98 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 1773 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4Q9M · Crystal structure of UPPs in complex with FPP and an allosteric inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DRB3 · AlphaFold monomer V2.0 prediction for isoprenyl transferase (Q8DRB3) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q8DRB3
- Elsewhere: RCSB PDB 4Q9M · PDBe 4Q9M · UniProt Q8DRB3
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