MolNFT v1 · #35243 · protein
Crystal structure of isocitrate dehydrogenase from sulfolobus tokodaii strain 7
2E5M · 409AA long hypothetical NADP-dependent isocitrate…: “Crystal structure of isocitrate dehydrogenase from sulfolobus tokodaii strain 7”. X-ray diffraction, 1 ligand (NAP), 8 pockets (best druggability 0.65). MolNFT v1 #35243 on…
- PDB
- 2E5M
- Type
- protein
- Length
- 806 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 409AA long hypothetical NADP-dependent isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- Q96YK6
- Ligands
- NAP
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 409AA long hypothetical NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) | protein | 403 | 44% helix, 20% strand | Q96YK6 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.65 | 0.88 | 24 | empty |
| 2 | 116 | 0.63 | 0.88 | 22 | empty |
| 3 | 368 | 0.56 | 0.75 | 45 | empty |
| 4 | 337 | 0.55 | 0.76 | 37 | empty |
| 5 | 256 | 0.54 | 0.76 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 2721 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 2E5M · Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain 7 · 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 Q96YK6
- Elsewhere: RCSB PDB 2E5M · PDBe 2E5M · UniProt Q96YK6
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