Research workbench
Structure and mechanism of action of isopentenylpyrophosphate- dimethylallylpyrophosphate isomerase: complex with nipp
Analyse Structure and mechanism of action of isopentenylpyrophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NFS
- 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
- DED, MN, MG
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase (EC 5.3.3.2) | protein | 176 | 27% 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
- DED · 2-dimethylamino-ethyl-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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.65 | 0.89 | 25 | MG, DED |
| 2 | 116 | 0.63 | 0.88 | 25 | DED |
| 3 | 64 | 0.37 | 0.78 | 20 | empty |
| 4 | 54 | 0.33 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 834 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1NFS · Structure and mechanism of action of isopentenylpyrophosphate-dimethylallylpyrophosphate… · 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 1NFS · PDBe 1NFS · UniProt Q46822
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