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Isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase in complex with the bromohydrine of ipp
Analyse Isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PPW
- Type
- protein
- Length
- 356 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.21
- Source
- Escherichia coli
- Molecule
- Isopentenyl-diphosphate delta-isomerase
- EC
- 5.3.3.2
- UniProt
- Q46822
- Ligands
- EIP, MN, MG
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · resolution 2.21 · 2 distinct chains · 26% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 176 | 25% helix, 33% strand | Q46822 |
| B | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 180 | 26% helix, 33% strand | Q46822 |
Ligands and binding sites
- EIP · 4-hydroxy-3-methyl butyl diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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 | 159 | 0.72 | 0.90 | 34 | MG, EIP |
| 2 | 128 | 0.70 | 0.91 | 31 | MG, EIP |
| 3 | 120 | 0.46 | 0.79 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 840 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1PPW · Isopentenylpyrophosphate-dimethylallylpyrophosphate isomerase in complex with the… · 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 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 Q46822
- Elsewhere: RCSB PDB 1PPW · PDBe 1PPW · UniProt Q46822
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