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Structure of HSICDH1:MG(II):ICT:NADPH(50%) complex reveals structural basis for observation of half-sites reactivity
Analyse Structure of HSICDH1:MG(II):ICT:NADPH(50%) complex reveals structural basis for… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PAY
- Type
- protein
- Length
- 1,635 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O75874
- Ligands
- ICT, NDP, MG
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 47% helix, 22% strand | O75874 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 412 | 48% helix, 22% strand | O75874 |
| C | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 408 | 48% helix, 22% strand | O75874 |
| D | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 406 | 47% helix, 22% strand | O75874 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · 4 copies · chains A, D, B, C
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, D
- MG · Magnesium ion · metal · 4 copies · chains A, D, B, C
- FMT · Formic acid · additive · 7 copies · chains A, B, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1004 | 0.80 | 0.81 | 101 | FMT |
| 2 | 1014 | 0.79 | 0.81 | 84 | ICT, NDP, FMT |
| 3 | 749 | 0.73 | 0.79 | 64 | ICT, MG |
| 4 | 680 | 0.71 | 0.78 | 62 | ICT, MG |
| 5 | 617 | 0.70 | 0.79 | 66 | ICT, MG |
Interfaces
3 interfaces between chains.
- A–D · 3701 Ų buried · 60 hydrogen bonds · protein-protein
- B–C · 3514 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 1138 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6PAY · Structure of HsICDH1:Mg(II):ICT:NADPH(50%) complex reveals structural basis for… · 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 O75874
- Elsewhere: RCSB PDB 6PAY · PDBe 6PAY · UniProt O75874
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