Research workbench
Crystal structure of human type I ipp isomerase complexed with a substrate analog
Analyse Crystal structure of human type I ipp isomerase complexed with a substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I6K
- Type
- protein
- Length
- 444 residues
- Chains
- 2
- 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
- EA2, MG, MN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) | protein | 224 | 33% helix, 30% strand | Q13907 |
| B | Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) | protein | 220 | 31% helix, 31% strand | Q13907 |
Ligands and binding sites
- EA2 · Aminoethanolpyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- ACY · Acetic acid · additive · 4 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 | 80 | 0.76 | 0.99 | 24 | MG, EA2 |
| 2 | 68 | 0.72 | 0.97 | 24 | MG, EA2 |
| 3 | 178 | 0.47 | 0.75 | 28 | ACY |
Interfaces
1 interface between chains.
- A–B · 363 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2I6K · Crystal structure of human type I IPP isomerase complexed with a substrate analog · 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 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 Q13907
- Elsewhere: RCSB PDB 2I6K · PDBe 2I6K · UniProt Q13907
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