Research workbench
3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium
Analyse 3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CNZ
- Type
- protein
- Length
- 726 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (3-isopropylmalate dehydrogenase)
- UniProt
- P37412
- Ligands
- MN, SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (3-isopropylmalate dehydrogenase) | protein | 363 | 48% helix, 20% strand | P37412 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.76 | 0.79 | 70 | MN, SO4 |
| 2 | 590 | 0.69 | 0.78 | 49 | MN, SO4 |
| 3 | 306 | 0.61 | 0.78 | 34 | empty |
| 4 | 302 | 0.57 | 0.76 | 30 | empty |
| 5 | 162 | 0.46 | 0.76 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 2531 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 1CNZ · 3-isopropylmalate dehydrogenase (ipmdh) from salmonella typhimurium · the same entry in another collection · chain A against A, TM-score 1.00
- P37412 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (P37412) · 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 P37412
- Elsewhere: RCSB PDB 1CNZ · PDBe 1CNZ · UniProt P37412
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.