Research workbench
Isph in complex with (E)-4-mercapto-3-methylbut-2-enyl diphosphate
Analyse Isph in complex with (E)-4-mercapto-3-methylbut-2-enyl diphosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H4E
- Type
- protein
- Length
- 619 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-3-methylbut-2-enyl diphosphate reductase
- EC
- 1.17.1.2
- UniProt
- P62623
- Ligands
- SF4, 10G
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 309 | 42% helix, 18% strand | P62623 |
| B | 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2) | protein | 310 | 43% helix, 18% strand | P62623 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 10G · (2E)-3-methyl-4-sulfanylbut-2-en-1-yl trihydrogen diphosphate · ligand · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.80 | 0.97 | 25 | SF4, 10G |
| 2 | 134 | 0.80 | 0.97 | 26 | SF4, 10G |
| 3 | 985 | 0.80 | 0.81 | 62 | empty |
| 4 | 308 | 0.65 | 0.81 | 46 | empty |
| 5 | 182 | 0.44 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 903 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4H4E · IspH in complex with (E)-4-mercapto-3-methylbut-2-enyl diphosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P62623 · AlphaFold monomer V2.0 prediction for 4-hydroxy-3-methylbut-2-enyl diphosphate reductase… · a predicted model of the same protein · chain A 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 P62623
- Elsewhere: RCSB PDB 4H4E · PDBe 4H4E · UniProt P62623
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.