Research workbench
Structure of human isopentenyl-diphosphate delta-isomerase 2
Analyse Structure of human isopentenyl-diphosphate delta-isomerase 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PNY
- Type
- protein
- Length
- 233 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl-diphosphate delta-isomerase 2
- EC
- 5.3.3.2
- UniProt
- Q9BXS1
- Ligands
- POP, CA, MN
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase 2 (EC 5.3.3.2) | protein | 233 | 33% helix, 28% strand | Q9BXS1 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · chains A
- CA · Calcium ion · metal · chains A
- MN · Manganese (II) ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.71 | 0.98 | 31 | CA, POP |
| 2 | 66 | 0.29 | 0.73 | 14 | empty |
Compared structures
- 2PNY · Structure of Human Isopentenyl-diphosphate Delta-isomerase 2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BXS1 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase 2 (Q9BXS1) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9BXS1
- Elsewhere: RCSB PDB 2PNY · PDBe 2PNY · UniProt Q9BXS1
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