MolNFT v1 · #14047 · protein
Crystal structure of NADP-dependent isocitrate dehydrogenase from porcine heart mitochondria
1LWD: “Crystal structure of NADP-dependent isocitrate dehydrogenase from porcine heart mitochondria”. X-ray diffraction, 3 ligands (ICT, MN, SO4), 10 pockets (best druggability 0.74). MolNFT v1 #14047 on GenesisL1: 3D structure, binding…
- PDB
- 1LWD
- Type
- protein
- Length
- 826 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- P33198
- Ligands
- ICT, MN, SO4
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 413 | 46% helix, 21% strand | P33198 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.74 | 0.80 | 62 | MN, ICT |
| 2 | 721 | 0.73 | 0.79 | 60 | MN, ICT |
| 3 | 58 | 0.73 | 0.99 | 26 | empty |
| 4 | 250 | 0.52 | 0.76 | 23 | empty |
| 5 | 225 | 0.51 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3548 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 1LWD · Crystal structure of NADP-dependent isocitrate dehydrogenase from porcine heart… · the same entry in another collection · chain A against A, TM-score 1.00
- P33198 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · 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 P33198
- Elsewhere: RCSB PDB 1LWD · PDBe 1LWD · UniProt P33198
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