MolNFT v1 · #149125 · protein
Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo form, in complex with its cofactor NADP+ and in complex with its substrate 6-phosphogluconate
6FQZ · 6-phosphogluconate dehydrogenase, decarboxylating: “Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo form, in complex with its cofactor NADP+…”. X-ray diffraction, 1 ligand (6PG), 11 pockets (best druggability…
- PDB
- 6FQZ
- Type
- protein
- Length
- 936 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phosphogluconate dehydrogenase, decarboxylating
- EC
- 1.1.1.44
- UniProt
- Q8IKT2
- Ligands
- 6PG
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | protein | 468 | 57% helix, 11% strand | Q8IKT2 |
Ligands and binding sites
- 6PG · 6-phosphogluconic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 19 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.73 | 0.98 | 23 | PEG |
| 2 | 444 | 0.71 | 0.81 | 50 | 6PG, GOL |
| 3 | 458 | 0.69 | 0.80 | 50 | 6PG |
| 4 | 53 | 0.68 | 0.97 | 22 | GOL |
| 5 | 321 | 0.62 | 0.79 | 38 | GOL |
Interfaces
1 interface between chains.
- A–B · 5614 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6FQZ · Plasmodium falciparum 6-phosphogluconate dehydrogenase in its apo form, 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 Q8IKT2
- Elsewhere: RCSB PDB 6FQZ · PDBe 6FQZ · UniProt Q8IKT2
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