Research workbench
Crystal structure of E.COLI isopentenyl DIPHOSPHATE:DIMETHYLALLYL diphosphate isomerase
Analyse Crystal structure of E.COLI isopentenyl DIPHOSPHATE:DIMETHYLALLYL diphosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HX3
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl diphosphate delta-isomerase
- EC
- 5.3.3.2
- UniProt
- Q46822
- Ligands
- MN, SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl diphosphate delta-isomerase (EC 5.3.3.2) | protein | 176 | 26% helix, 34% strand | Q46822 |
| B | Isopentenyl diphosphate delta-isomerase (EC 5.3.3.2) | protein | 180 | 26% helix, 33% strand | Q46822 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.64 | 0.88 | 24 | SO4, IMD |
| 2 | 105 | 0.63 | 0.88 | 26 | SO4, IMD |
| 3 | 124 | 0.46 | 0.78 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 828 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 1HX3 · Crystal structure of E.COLI isopentenyl DIPHOSPHATE:DIMETHYLALLYL diphosphate isomerase · the same entry in another collection · chain A against A, TM-score 1.00
- Q46822 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase (Q46822) · 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 Q46822
- Elsewhere: RCSB PDB 1HX3 · PDBe 1HX3 · UniProt Q46822
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