MolNFT v1 · #19443 · protein
X-ray structure of human glucose 6-phosphate dehydrogenase (variant canton R459L) complexed with structural NADP+
1QKI · Glucose-6-phosphate 1-dehydrogenase: “X-ray structure of human glucose 6-phosphate dehydrogenase (variant canton R459L) complexed with structural…”. X-ray diffraction, 2 ligands (NAP, GOA), 20 pockets (best druggability 0.86).…
- PDB
- 1QKI
- Type
- protein
- Length
- 3,912 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-6-phosphate 1-dehydrogenase
- EC
- 1.1.1.49
- UniProt
- P11413
- Ligands
- NAP, GOA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 488 | 38% helix, 20% strand | P11413 |
| B, C | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 489 | 36% helix, 21% strand | P11413 |
| D | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 490 | 38% helix, 21% strand | P11413 |
| E | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 487 | 37% helix, 21% strand | P11413 |
| F | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 491 | 37% helix, 21% strand | P11413 |
| G, H | Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49) | protein | 489 | 36% helix, 21% strand | P11413 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOA · Glycolic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 5 copies · chains A, B, D, C, E, G, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1166 | 0.86 | 0.88 | 124 | empty |
| 2 | 1113 | 0.86 | 0.88 | 126 | empty |
| 3 | 783 | 0.74 | 0.79 | 78 | NAP |
| 4 | 797 | 0.74 | 0.79 | 72 | NAP |
| 5 | 765 | 0.73 | 0.79 | 70 | NAP |
Interfaces
16 interfaces between chains.
- E–F · 2927 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 2900 Ų buried · 48 hydrogen bonds · protein-protein
- C–D · 2888 Ų buried · 47 hydrogen bonds · protein-protein
- G–H · 2843 Ų buried · 48 hydrogen bonds · protein-protein
- A–E · 885 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1QKI · X-ray structure of human glucose 6-phosphate dehydrogenase (variant canton R459L)… · the same entry in another collection · chain H against H, TM-score 1.00
- P11413 · AlphaFold monomer V2.0 prediction for glucose-6-phosphate 1-dehydrogenase (P11413) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P11413
- Elsewhere: RCSB PDB 1QKI · PDBe 1QKI · UniProt P11413
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