Research workbench
Crystal structure of NAD dependent isocitrate dehydrogenase from acidithiobacillus thiooxidans
Analyse Crystal structure of NAD dependent isocitrate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D4V
- Type
- protein
- Length
- 1,708 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- UniProt
- Q8GAX0
- Ligands
- NAD
- Pockets
- 15 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate dehydrogenase | protein | 427 | 46% helix, 19% strand | Q8GAX0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- FLC · Citrate anion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.75 | 0.80 | 62 | FLC, NAD |
| 2 | 789 | 0.75 | 0.80 | 71 | FLC, NAD |
| 3 | 725 | 0.75 | 0.80 | 60 | FLC, NAD |
| 4 | 786 | 0.75 | 0.80 | 66 | FLC, NAD |
| 5 | 530 | 0.64 | 0.76 | 53 | empty |
Interfaces
3 interfaces between chains.
- A–B · 4067 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 4052 Ų buried · 61 hydrogen bonds · protein-protein
- A–D · 530 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2D4V · Crystal structure of NAD dependent isocitrate dehydrogenase from Acidithiobacillus… · 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 Q8GAX0
- Elsewhere: RCSB PDB 2D4V · PDBe 2D4V · UniProt Q8GAX0
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