MolNFT v1 · #122892 · protein
Isopropylmalate dehydrogenase in complex with isopropylmalate
5J32 · 3-isopropylmalate dehydrogenase 2, chloroplastic: “Isopropylmalate dehydrogenase in complex with isopropylmalate”. X-ray diffraction, 2 ligands (IPM, MG), 16 pockets (best druggability 0.74). MolNFT v1 #122892 on GenesisL1: 3D…
- PDB
- 5J32
- Type
- protein
- Length
- 1,450 residues
- Chains
- 4
- 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
- IPM, MG
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 369 | 47% helix, 22% strand | P93832 |
| B | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 365 | 49% helix, 21% strand | P93832 |
| C | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 356 | 49% helix, 21% strand | P93832 |
| D | 3-isopropylmalate dehydrogenase 2, chloroplastic (EC 1.1.1.85) | protein | 360 | 48% helix, 22% strand | P93832 |
Ligands and binding sites
- IPM · 3-isopropylmalic acid · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.74 | 0.81 | 52 | MG, IPM |
| 2 | 563 | 0.72 | 0.81 | 51 | MG, IPM |
| 3 | 530 | 0.72 | 0.81 | 46 | MG, IPM |
| 4 | 584 | 0.72 | 0.80 | 55 | MG, IPM |
| 5 | 238 | 0.62 | 0.81 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2584 Ų buried · 52 hydrogen bonds · protein-protein
- C–D · 2501 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 428 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5J32 · Isopropylmalate dehydrogenase in complex with isopropylmalate · the same entry in another collection · chain D against D, TM-score 1.00
- P93832 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase 2, chloroplastic… · a predicted model of the same protein · chain C against A, TM-score 1.00
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 5J32 · PDBe 5J32 · UniProt P93832
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