Research workbench
Crystal structure of isocitrate dehydrogenase-2 in complex with NADP(+) from mycobacterium tuberculosis
Analyse Crystal structure of isocitrate dehydrogenase-2 in complex with NADP(+) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KVU
- Type
- protein
- Length
- 2,942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase
- EC
- 1.1.1.42
- UniProt
- O53611
- Ligands
- NAP, MLT
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 738 | 47% helix, 17% strand | O53611 |
| B | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 738 | 47% helix, 17% strand | O53611 |
| C | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 734 | 47% helix, 17% strand | O53611 |
| D | Isocitrate dehydrogenase (EC 1.1.1.42) | protein | 732 | 46% helix, 17% strand | O53611 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- MLT · D-malate · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, D, B, C
- MLA · Malonic acid · additive · 2 copies · chains B, D
- GOL · Glycerol · additive · 2 copies · chains C, D
- SIN · Succinic acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.86 | 0.87 | 102 | NAP, SIN |
| 2 | 1038 | 0.82 | 0.83 | 91 | NAP, MLT |
| 3 | 1033 | 0.81 | 0.82 | 81 | NAP, MLA |
| 4 | 1042 | 0.80 | 0.82 | 82 | NAP, MLA, EDO |
| 5 | 117 | 0.79 | 0.97 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–D · 1023 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1004 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 403 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 317 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5KVU · Crystal structure of isocitrate dehydrogenase-2 in complex with NADP(+) from… · 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 O53611
- Elsewhere: RCSB PDB 5KVU · PDBe 5KVU · UniProt O53611
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.