Research workbench
Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with ipm and mn
Analyse Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y41
- Type
- protein
- Length
- 692 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- Q5SIY4
- Ligands
- IPM, MN
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 346 | 49% helix, 19% strand | Q5SIY4 |
Ligands and binding sites
- IPM · 3-isopropylmalic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.76 | 0.99 | 22 | empty |
| 2 | 643 | 0.72 | 0.80 | 58 | IPM, MN |
| 3 | 546 | 0.71 | 0.80 | 56 | IPM |
| 4 | 237 | 0.67 | 0.83 | 33 | empty |
| 5 | 270 | 0.64 | 0.81 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2559 Ų buried · 59 hydrogen bonds · protein-protein
Compared structures
- 2Y41 · Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with IPM… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SIY4 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (Q5SIY4) · 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 Q5SIY4
- Elsewhere: RCSB PDB 2Y41 · PDBe 2Y41 · UniProt Q5SIY4
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