Research workbench
Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and mn
Analyse Crystal structure of the monomeric isocitrate dehydrogenase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ITW
- Type
- protein
- Length
- 2,959 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- P16100
- Ligands
- ICT, MN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 740 | 48% helix, 17% strand | P16100 |
| C | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 739 | 48% helix, 17% strand | P16100 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.80 | 0.99 | 24 | empty |
| 2 | 117 | 0.80 | 0.98 | 24 | empty |
| 3 | 110 | 0.80 | 0.98 | 23 | empty |
| 4 | 111 | 0.79 | 0.98 | 23 | empty |
| 5 | 899 | 0.76 | 0.79 | 106 | MN, ICT |
Interfaces
4 interfaces between chains.
- A–D · 651 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 162 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 140 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1ITW · Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate… · the same entry in another collection · chain B against B, TM-score 1.00
- P16100 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P16100) · a predicted model of the same protein · chain A 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 P16100
- Elsewhere: RCSB PDB 1ITW · PDBe 1ITW · UniProt P16100
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