MolNFT v1 · #54920 · protein
Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with NADH and mn
2Y42 · 3-isopropylmalate dehydrogenase: “Structure of isopropylmalate dehydrogenase from thermus thermophilus - complex with NADH and mn”. X-ray diffraction, 3 ligands (BCN, NAD, MN), 13 pockets (best druggability 0.82). MolNFT v1 #54920…
- PDB
- 2Y42
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- Q5SIY4
- Ligands
- BCN, NAD, MN
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 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 | 45% helix, 20% strand | Q5SIY4 |
| B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 350 | 48% helix, 18% strand | Q5SIY4 |
| C | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 352 | 48% helix, 21% strand | Q5SIY4 |
| D | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 355 | 46% helix, 21% strand | Q5SIY4 |
Ligands and binding sites
- BCN · Bicine · ligand · 5 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 783 | 0.82 | 0.85 | 76 | empty |
| 2 | 624 | 0.73 | 0.80 | 53 | BCN, NAD, MN |
| 3 | 67 | 0.71 | 0.96 | 19 | empty |
| 4 | 103 | 0.68 | 0.91 | 23 | empty |
| 5 | 637 | 0.68 | 0.77 | 43 | BCN, MN |
Interfaces
4 interfaces between chains.
- A–B · 2268 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 2196 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 730 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 92 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2Y42 · Structure of Isopropylmalate dehydrogenase from Thermus thermophilus - complex with NADH… · the same entry in another collection · chain D against D, TM-score 1.00
- Q5SIY4 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (Q5SIY4) · a predicted model of the same protein · chain B 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 Q5SIY4
- Elsewhere: RCSB PDB 2Y42 · PDBe 2Y42 · UniProt Q5SIY4
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