Research workbench
Crystal structure of human ipp isomerase I in space group P212121
Analyse Crystal structure of human ipp isomerase I in space group P212121 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DHO
- Type
- protein
- Length
- 215 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopentenyl-diphosphate delta-isomerase 1
- EC
- 5.3.3.2
- UniProt
- Q13907
- Ligands
- MN, NA, CL
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) | protein | 215 | 30% helix, 32% strand | Q13907 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 8 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 10 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 | 243 | 0.65 | 0.82 | 38 | CL |
| 2 | 67 | 0.31 | 0.75 | 12 | empty |
Compared structures
- 2DHO · Crystal structure of human IPP isomerase I in space group P212121 · the same entry in another collection · chain A against A, TM-score 1.00
- Q13907 · AlphaFold monomer V2.0 prediction for isopentenyl-diphosphate delta- isomerase 1 (Q13907) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q13907
- Elsewhere: RCSB PDB 2DHO · PDBe 2DHO · UniProt Q13907
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