MolNFT v1 · #104411 · protein
Crystal structure of upps in complex with fpp and an allosteric inhibitor
4Q9M · Isoprenyl transferase: “Crystal structure of upps in complex with fpp and an allosteric inhibitor”. X-ray diffraction, 3 ligands (2ZW, FPP, CD), 3 pockets (best druggability 0.83). MolNFT v1 #104411 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.