MolNFT v1 · #54917 · protein
Structure of isopropylmalate dehydrogenase from thermus thermophilus - apo enzyme
2Y3Z · 3-isopropylmalate dehydrogenase: “Structure of isopropylmalate dehydrogenase from thermus thermophilus - apo enzyme”. X-ray diffraction, 1 pocket (best druggability 0.45). MolNFT v1 #54917 on GenesisL1: 3D structure, binding sites…
- PDB
- 2Y3Z
- Type
- protein
- Length
- 351 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- Q5SIY4
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 351 | 48% helix, 17% strand | Q5SIY4 |
Ligands and binding sites
- 2PE · Nonaethylene glycol · additive · 3 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.45 | 0.74 | 30 | 2PE, GOL |
Compared structures
- 2Y3Z · Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - apo enzyme · 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 0.93
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 2Y3Z · PDBe 2Y3Z · UniProt Q5SIY4
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