Research workbench
Crystal structure of an isocitrate dehydrogenase from sinorhizobium meliloti 1021
Analyse Crystal structure of an isocitrate dehydrogenase from sinorhizobium meliloti… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3US8
- Type
- protein
- Length
- 802 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- Q92PG6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 401 | 47% helix, 22% strand | Q92PG6 |
| B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 401 | 47% helix, 22% strand | Q92PG6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.76 | 0.81 | 79 | SO4 |
| 2 | 860 | 0.74 | 0.79 | 72 | empty |
| 3 | 275 | 0.54 | 0.76 | 34 | empty |
| 4 | 210 | 0.52 | 0.77 | 26 | empty |
| 5 | 56 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3524 Ų buried · 37 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3US8 · Crystal Structure of an isocitrate dehydrogenase from Sinorhizobium meliloti 1021 · the same entry in another collection · 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 Q92PG6
- Elsewhere: RCSB PDB 3US8 · PDBe 3US8 · UniProt Q92PG6
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