Research workbench
Structure of Y104F idi-1 mutant in complex with eipp
Analyse Structure of Y104F idi-1 mutant in complex with eipp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B2K
- 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
- EIP, MN, MG
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 25% 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, 34% 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
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 | 147 | 0.71 | 0.91 | 34 | MG, EIP |
| 2 | 130 | 0.70 | 0.91 | 32 | MG, EIP |
| 3 | 57 | 0.36 | 0.79 | 21 | empty |
| 4 | 60 | 0.34 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 840 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2B2K · structure of Y104F IDI-1 mutant in complex with EIPP · 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 2B2K · PDBe 2B2K · UniProt Q46822
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