Research workbench
Crystal structure of isocitrate dehydrogenase from bacillus subtilis
Analyse Crystal structure of isocitrate dehydrogenase from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HQS
- Type
- protein
- Length
- 846 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- P39126
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 423 | 48% helix, 19% strand | P39126 |
Ligands and binding sites
- PGO · S-1,2-propanediol · additive · 5 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
- PGR · R-1,2-propanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.76 | 0.80 | 81 | CIT, PGO |
| 2 | 785 | 0.75 | 0.80 | 75 | PGR, CIT |
| 3 | 319 | 0.65 | 0.80 | 43 | PGO |
| 4 | 342 | 0.65 | 0.80 | 45 | PGO |
| 5 | 100 | 0.41 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 3774 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 1HQS · Crystal structure of isocitrate dehydrogenase from bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- P39126 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P39126) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P39126
- Elsewhere: RCSB PDB 1HQS · PDBe 1HQS · UniProt P39126
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