MolNFT v1 · #54918 · protein
Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with mn
2Y40 · 3-isopropylmalate dehydrogenase: “Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with mn”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.69). MolNFT v1 #54918 on GenesisL1: 3D…
- PDB
- 2Y40
- 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
- MN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 347 | 47% helix, 20% strand | Q5SIY4 |
| B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 345 | 46% helix, 19% strand | Q5SIY4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 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 | 94 | 0.69 | 0.92 | 23 | empty |
| 2 | 77 | 0.61 | 0.89 | 22 | empty |
| 3 | 424 | 0.59 | 0.75 | 40 | MN |
| 4 | 320 | 0.53 | 0.75 | 39 | empty |
| 5 | 60 | 0.27 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2280 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 2Y40 · Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with Mn · 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 0.94
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 2Y40 · PDBe 2Y40 · UniProt Q5SIY4
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