MolNFT v1 · #104413 · protein
Crystal structure of upps + inhibitor
4Q9O · Isoprenyl transferase: “Crystal structure of upps + inhibitor”. X-ray diffraction, 2 ligands (2ZW, SO4), 6 pockets (best druggability 0.81). MolNFT v1 #104413 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4Q9O
- Type
- protein
- Length
- 469 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, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoprenyl transferase (EC 2.5.1.-) | protein | 240 | 51% helix, 15% strand | Q8DRB3 |
| B | Isoprenyl transferase (EC 2.5.1.-) | protein | 229 | 54% 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
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.81 | 0.88 | 47 | 2ZW, SO4 |
| 2 | 461 | 0.81 | 0.88 | 50 | 2ZW, SO4 |
| 3 | 62 | 0.73 | 0.98 | 26 | empty |
| 4 | 52 | 0.30 | 0.76 | 14 | empty |
| 5 | 58 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1816 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
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 4Q9O · PDBe 4Q9O · UniProt Q8DRB3
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