Research workbench
Isopropylmalate dehydrogenase in complex with NAD+
Analyse Isopropylmalate dehydrogenase in complex with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J33
- Type
- protein
- Length
- 2,868 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase 2, chloroplastic
- EC
- 1.1.1.85
- UniProt
- P93832
- Ligands
- NAD, MG, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 360 | 46% helix, 23% strand | P93832 |
| B, C, E, F, G | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 359 | 47% helix, 23% strand | P93832 |
| D | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 358 | 47% helix, 22% strand | P93832 |
| H | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 355 | 46% helix, 19% strand | P93832 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, H, D, F, E, G
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, H, D, F, E, G
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, H, D, F, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.83 | 0.84 | 110 | NAD, SO4, MG |
| 2 | 1020 | 0.83 | 0.84 | 109 | NAD, SO4, MG |
| 3 | 510 | 0.75 | 0.83 | 48 | MG, NAD, SO4 |
| 4 | 507 | 0.75 | 0.83 | 51 | NAD, SO4, MG |
| 5 | 530 | 0.75 | 0.83 | 48 | NAD, SO4, MG |
Interfaces
7 interfaces between chains.
- C–H · 2714 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2689 Ų buried · 50 hydrogen bonds · protein-protein
- D–F · 2652 Ų buried · 49 hydrogen bonds · protein-protein
- E–G · 2650 Ų buried · 53 hydrogen bonds · protein-protein
- A–D · 598 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5J33 · Isopropylmalate dehydrogenase in complex with NAD+ · the same entry in another collection · chain H against H, TM-score 1.00
- P93832 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase 2, chloroplastic… · 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 P93832
- Elsewhere: RCSB PDB 5J33 · PDBe 5J33 · UniProt P93832
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