Research workbench
Crystal structure of trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with NADP+, isocitrate and CA2+
Analyse Crystal structure of trypanosoma cruzi cytosolic isocitrate dehydrogenase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AJC
- Type
- protein
- Length
- 3,301 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- Q4E4L7
- Ligands
- NAP, ICT, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 413 | 47% helix, 21% strand | Q4E4L7 |
| B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 412 | 46% helix, 20% strand | Q4E4L7 |
| H | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 411 | 46% helix, 21% strand | Q4E4L7 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ICT · Isocitric acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 893 | 0.84 | 0.86 | 109 | NAP, ICT |
| 2 | 1130 | 0.82 | 0.83 | 117 | NAP, ICT |
| 3 | 557 | 0.81 | 0.87 | 67 | NAP, ICT |
| 4 | 571 | 0.80 | 0.86 | 73 | NAP, ICT |
| 5 | 912 | 0.79 | 0.81 | 69 | NAP, ICT |
Interfaces
14 interfaces between chains.
- E–F · 4102 Ų buried · 64 hydrogen bonds · protein-protein
- G–H · 4100 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 4075 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 4034 Ų buried · 64 hydrogen bonds · protein-protein
- E–G · 591 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6AJC · Crystal structure of Trypanosoma cruzi cytosolic isocitrate dehydrogenase in complex with… · 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 Q4E4L7
- Elsewhere: RCSB PDB 6AJC · PDBe 6AJC · UniProt Q4E4L7
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