Research workbench
Structure of isopropylmalate dehydrogenase from thermus thermophilus in complex with ipm, mn and NADH
Analyse Structure of isopropylmalate dehydrogenase from thermus thermophilus in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F7I
- Type
- protein
- Length
- 1,397 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
- IPM, NAD, K, MN
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 350 | 48% helix, 19% strand | Q5SIY4 |
| C | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 348 | 48% helix, 19% strand | Q5SIY4 |
| D | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 349 | 48% helix, 19% strand | Q5SIY4 |
Ligands and binding sites
- IPM · 3-isopropylmalic acid · ligand · 4 copies · chains A, B, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 7 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 29 copies · chains A, B, C, D
- EOH · Ethanol · additive · 6 copies · chains A, B, C, D
- MPO · 3[N-morpholino]propane sulfonic acid · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.82 | 0.86 | 89 | IPM, NAD, GOL, EOH |
| 2 | 675 | 0.81 | 0.85 | 81 | IPM, NAD, MN, GOL |
| 3 | 648 | 0.76 | 0.82 | 61 | IPM, NAD, GOL, EOH |
| 4 | 218 | 0.75 | 0.89 | 32 | MPO, GOL |
| 5 | 230 | 0.75 | 0.89 | 32 | GOL |
Interfaces
5 interfaces between chains.
- A–B · 2680 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 2606 Ų buried · 58 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 258 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 192 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4F7I · Structure of Isopropylmalate dehydrogenase from Thermus thermophilus in 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 D 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 4F7I · PDBe 4F7I · UniProt Q5SIY4
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